Immune profiling by primer extension target enrichment

ABSTRACT

Methods and compositions are described herein for primer extension target enrichment of immune receptor (BCR or TCR) sequences.

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

This application is a continuation of application Ser. No. 16/996,733 filed on Aug. 18, 2020, which is a continuation in part of application Ser. No. 15/611,507, filed on Jun. 1, 2017, now U.S. Pat. No. 11,098,360 issued Aug. 24, 2021, which claims benefit of priority to U.S. Provisional Patent Application No. 62/344,330, filed on Jun. 1, 2016, each of which is incorporated herein by reference for all purposes.

REFERENCE TO A SEQUENCE LISTING

The Sequence Listing written in file 098599-1391905_SL.xml created on Jul. 14, 2023; 676,027 bytes, is hereby incorporated by reference in its entirety for all purposes. The instant application contains a Sequence Listing which has been submitted electronically in XML file format.

BACKGROUND OF THE INVENTION

The adaptive immune system can generate a wide array of diverse binding molecules. For example, recombination, random insertion, deletion and substitution, has the potential to create between 10¹⁵ and 10²⁰ T-cell receptor (TCR) clonotypes and considerably more B cell receptor (BCR) clonotypes due to the greater number of VDJ sequences as well as somatic hypermutation. Naïve B or T cell clonotypes can be subject to positive and negative selection pressures, where cells expressing certain immune receptor sequences are expanded or deleted respectively. As such, the repertoire of BCR or TCR sequences can include information regarding immunological development, diseases state, the status of an organ transplant (e.g., tolerated or rejected), or the presence or absence of an autoimmune disorder, cancer, or infection. Moreover, high throughput sequencing of BCR or TCR repertoires has become a powerful tool to study or monitor basic immunology, disease state, autoimmune disorders, cancer, infection, organ transplantation and the like.

BRIEF SUMMARY OF THE INVENTION

Described herein are improved methods and compositions for primer extension target enrichment (PETE) of immune receptor (TCR or BCR, or a combination thereof) sequences. Methods and compositions described herein can be used, e.g., for high-throughput sequencing and/or immune repertoire profiling. In some cases, the methods and compositions described herein can provide increased sensitivity, decreased background, or increased efficiency in high-throughput sequencing library preparation of immune receptor polynucleotides. In some cases, the methods and compositions described herein can provide increased detection of rare immune cell clonotypes, reduced sample requirements, or a combination thereof. In some embodiments, the improvement is provided by the sequential use of two flanking primers for enrichment of immune receptor sequences by PETE, where a first flanking primer hybridizes to a target polynucleotide and is extended with a polymerase, and a second flanking primer hybridizes to the extended first flanking primer and is extended with a polymerase. Thus, the sample is enriched for target polynucleotides containing the first primer hybridization site and a complement of the second primer hybridization site.

In a first aspect, the present invention provides a composition comprising: i) a plurality of structurally distinct immune cell receptor V gene specific primers, wherein the plurality comprises at least 10 structurally distinct primers having the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [FW], wherein: [5′-Phos] comprises a 5′ phosphate; [SPLINT] comprises an adaptor hybridization site of 2-8 nucleotides in length; [BARCODE] comprises a barcode region of at least 6 nucleotides in length, wherein each nucleotide of the barcode region is independently selected from the group consisting of N and W; and [FW] of each immune cell receptor V gene specific primer comprises a structurally distinct region that specifically hybridizes to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene.

In some embodiments, [BARCODE] comprises a barcode region of from 6 to 16 nucleotides in length. In some embodiments, the [FW] of each immune cell receptor V gene specific primer specifically hybridizes to a framework 1, framework 2, or framework 3 region of a T cell receptor V gene. In some embodiments, the [FW] of each immune cell receptor V gene specific primer specifically hybridizes to a framework 1, framework 2, or framework 3 region of a B cell receptor V gene. In some embodiments, the plurality comprises at least 10 of the primers set forth in SEQ ID Nos:1-121.

In some embodiments, the [SPLINT] consists of 6 consecutive nucleotides, preferably of the sequence CGA TCT. In some embodiments, [BARCODE] consists of thirteen consecutive nucleotides selected from the group consisting of N and W, preferably of the sequence WNN NNN WNN NNN W (SEQ ID NO:524). In some embodiments, the composition comprises at least 50, preferably all of the primers set forth in SEQ ID NOs:1-121.

In a second aspect, the present invention provides a reaction mixture comprising: i) a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality each comprise immune cell receptor V gene regions, optionally D gene regions, optionally C gene regions, and J gene regions; and ii) a plurality of immune cell receptor V gene specific primers according to any one of the preceding aspects or embodiments. In some embodiments, the plurality of immune cell receptor V gene specific primers are each hybridized to one of the plurality of structurally different target polynucleotides.

In some embodiments, a portion of the individual target polynucleotides of the plurality each comprise immune cell receptor D gene regions and a portion of the individual target polynucleotides of the plurality do not comprise immune cell receptor D gene regions. In some embodiments, the individual target polynucleotides of the plurality each comprise immune cell receptor D gene regions. In some embodiments, a portion of the individual target polynucleotides of the plurality each comprise immune cell receptor C gene regions and a portion of the individual target polynucleotides of the plurality do not comprise immune cell receptor C gene regions. In some embodiments, the individual target polynucleotides of the plurality each comprise immune cell receptor C gene regions. In some embodiments, the reaction mixture comprises a plurality of immune cell receptor C gene specific (C-segment) primers. In some embodiments, the plurality of immune cell receptor C gene specific primers are hybridized to one of the structurally different target polynucleotides.

In a third aspect, the present invention provides a reaction mixture comprising: i) a plurality of immune cell receptor specific first primer extension products, wherein the individual first primer extension products each comprise the following from regions from 5′ to 3′: a sequencer-specific adapter sequence, optionally a multiplex identifier (MID) barcode, a unique molecular identifier (UID) barcode, at least a portion of an immune cell receptor framework 3 region, an immune cell receptor CDR3 region, an optional immune cell receptor diversity (D) region, an optional immune cell receptor constant (C) region, and at least a portion of an immune cell receptor J region; and ii) a plurality of J-gene specific primers, wherein each of the plurality of J-gene specific primers is hybridized to the immune cell receptor J region of one of the individual first primer extension products or a plurality of C gene specific primers, wherein each of the plurality of C gene specific primers is hybridized to the immune cell receptor C region of one of the individual first primer extension products.

In some embodiments, the reaction mixture further comprises a DNA polymerase. In some embodiments, the individual first primer extension products each comprise the multiplex identifier (MID) barcode. In some embodiments, a portion of the individual first primer extension products comprise the immune cell receptor D region and a portion of the first primer extension products do not comprise the immune cell receptor D region. In some embodiments, the individual target polynucleotides each comprise the immune cell receptor D region. In some embodiments, the plurality of J-gene specific primers comprise at least 10 of the primers set forth in SEQ ID Nos:122-204. In some embodiments, the plurality of J-gene specific primers comprise at least 50, preferably all of the primers set forth in SEQ ID Nos: 122-204. In some embodiments, the individual target polynucleotides each comprise the immune cell receptor C region. In some embodiments, the plurality of C gene specific primers comprise at least two of the primers set forth in SEQ ID NOs:205-213. In some embodiments, the plurality of C gene specific primers comprise at least five, preferably all, of the primers set forth in SEQ ID NOs:205-213.

In a fourth aspect, the present invention provides a reaction mixture comprising: i) a plurality of first primer extension products, the individual first primer extension products each comprising the following from 5′ to 3′: a) a 5′ phosphate; b) a SPLINT region comprising an adaptor hybridization site of 2-8 nucleotides in length; c) a unique molecular identifier (UID) barcode; d) at least a portion of an immune cell receptor framework 3 region; e) an immune cell receptor CDR3 region; f) an optional immune cell receptor diversity region; g) at least a portion of an immune cell receptor J region; and h) an optional immune cell receptor constant region; and i) a plurality of double-stranded splint adapters, each comprising: a) a 5′ single-stranded overhang region hybridized to the SPLINT region of an individual first primer extension product; b) optionally a multiplex identifier (MID) barcode; and c) a sequencer-specific universal primer sequence.

In some embodiments, the reaction mixture further comprises ligase. In some embodiments, the double-stranded splint adapters each comprise a multiplex identifier (MID) barcode.

In a fifth aspect, the present invention provides a method for enriching from a sample a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality comprise immune cell receptor V, J, and optionally C and/or D gene regions, the method comprising: a) providing a reaction mixture according to any one of the preceding aspects or embodiments that provide a reaction mixture, wherein the immune cell receptor V gene specific primers are hybridized to the V gene regions of the target polynucleotides; b) extending the hybridized immune cell receptor V gene specific primers with a polymerase, and then removing un-extended immune cell receptor V gene specific primers, if present, wherein the extended immune cell receptor V gene specific primers comprise at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region; c) hybridizing a first universal adaptor to the [SPLINT] adaptor hybridization site of the extended immune cell receptor V gene specific primers; d) ligating the hybridized first universal adapters to the extended immune cell receptor V gene specific primers, and then removing un-ligated adapters, if present; e) hybridizing a plurality of immune cell receptor J gene specific primers to the J region portions of the extended immune cell receptor V gene specific primers, wherein the immune cell receptor J gene specific primers comprise a 3′ J gene hybridizing region and a 5′ second universal adapter region; and f) extending the hybridized immune cell receptor J gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region flanked by a first and second universal adapter sequence.

In some embodiments, e) and f) are repeated 2 to 15 times by heating to denature double-stranded products, cooling to hybridize un-extended immune cell receptor J gene specific primers to the J region portions of the extended immune cell receptor V gene specific primers, and extending hybridized primers. In some embodiments, the removing un-extended immune cell receptor V gene specific primers comprises digesting single-stranded DNA exonuclease digestion. In some embodiments, the method further comprises amplifying double-stranded products comprising first and second universal adapters by universal PCR. In some embodiments, the structurally different target polynucleotides are cDNA. In some embodiments, prior to step a), a cDNA synthesis step is included to prepare cDNA from total RNA or mRNA. In some embodiments, step e) is modified such that the plurality of immune cell receptor J gene specific primers are substituted for a plurality of immune cell receptor C gene specific primers, thereby forming a plurality of structurally different double-stranded products, each comprising at least a portion of the immune cell receptor V region and at least a portion of the immune cell receptor C region.

In some embodiments, the invention is a method for enriching a sample for a plurality of structurally different target polynucleotides comprising an immune gene sequence the method comprising: a) contacting a sample with a plurality of immune cell receptor V gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT1], [BARCODE], and [V], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT] is a first adaptor sequence; [BARCODE] is a unique molecular identifier barcode; and [V] is a sequence capable of hybridizing to an immune cell receptor V gene; b) hybridizing and extending the V gene specific primers to form a plurality of first double-stranded primer extension products; c) contacting the sample with an exonuclease to remove unhybridized V gene specific primers from the first double stranded primer extension products; d) contacting the sample with a plurality of immune cell receptor J gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT2], and [J], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT2] is a second adaptor sequence; and [J] is a sequence capable of hybridizing to an immune cell receptor J gene; and further contacting the sample with a first universal primer capable of hybridizing to the first adaptor sequence; e) hybridizing and extending the J gene specific primers and the first universal primer to form a plurality of second double-stranded primer extension products; f) contacting the sample with an exonuclease to remove unhybridized J gene specific primers and first universal primer from the second double-stranded primer extension products; g) contacting the sample with first and second universal primers capable of hybridizing to the first and second adaptor sequences; h) amplifying the plurality of second double-stranded primer extension products thereby enriching the plurality of structurally different target polynucleotides comprising an immune gene sequence. In some embodiments, the immune genes comprise one or more of T-cell receptor alpha (TCRA), T-cell receptor beta (TCRB), T-cell receptor gamma (TCRG), T-cell receptor delta (TCRD), Immunoglobulin heavy chain (IGH) and Immunoglobulin light chain lambda or kappa (IGL and IGK). In some embodiments, the plurality of V gene specific primers and the plurality of J gene specific primers include primers from Table 2a

In some embodiments, the hybridizing in steps b) and/or e) comprises one or more cycles of a step-wise temperature drop of two or more steps, for example, 20 cycles of temperature change from 60° C. to 57.5° C. and to 55° C. In some embodiments, hybridizing and extending in step e) comprises two or more cycles of duplex denaturation, primer annealing and primer extension, for example hybridizing and extending in step e) comprises 10 cycles temperature change from >90° C., to 60° C. to 57.5° C., to 55° C. and to 72° C.

In some embodiments, the first and second universal primers in step g) comprise additional 5′sequences not present in the first and second adaptors but the first universal primer in step d) does not comprise additional 5′sequences not present in the first adaptor.

In some embodiments the exonuclease in steps c) and/or f) is thermolabile, e.g., a thermolabile Exonuclease I.

In some embodiments, extending in steps b) and/or e) is with a high-fidelity DNA polymerase.

In some embodiments, the method comprises a purification step after steps c) and/or h) but not between steps f) and g). In some embodiments, the first and second universal primers comprise a modification preventing digestion of the primers with the exonuclease, e.g., a phosphorothioate (PS) bond, a 2′-O-methyl (2′OMe), a 2′-fluoride and Inverted ddT. In some embodiments, the V-gene specific primers, the J-gene specific primers and the first universal primer in step d) do not comprise a modification preventing digestion of the primers with the exonuclease.

In some embodiments, the method further comprises sequencing the plurality of structurally different target polynucleotides comprising an immune gene sequence.

In some embodiments, the invention is a method for contamination-reduced sequencing a plurality of structurally different target polynucleotides comprising an immune gene sequence the method comprising: a) contacting a sample with a plurality of immune cell receptor V gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT1], [BARCODE], and [V], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT] is a first adaptor sequence; [BARCODE] is a unique molecular identifier barcode (UMI); and [V] is a sequence capable of hybridizing to an immune cell receptor V gene; b) hybridizing and extending the V gene specific primers to form a plurality of first double-stranded primer extension products; c) contacting the sample with an exonuclease to remove unhybridized V gene specific primers from the first double stranded primer extension products; d) contacting the sample with a plurality of immune cell receptor J gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT2], and [J], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT2] is a second adaptor sequence; and [J] is a sequence capable of hybridizing to an immune cell receptor J gene; and further contacting the sample with a first universal primer capable of hybridizing to the first adaptor sequence; e) hybridizing and extending the J gene specific primers and the first universal primer to form a plurality of second double-stranded primer extension products; f) contacting the sample with an exonuclease to remove unhybridized J gene specific primers and first universal primer from the second double-stranded primer extension products; g) contacting the sample with first and second universal primers capable of hybridizing to the first and second adaptor sequences; h) amplifying the plurality of second double-stranded primer extension products thereby enriching the plurality of structurally different target polynucleotides comprising an immune gene sequence; i) sequencing the plurality of structurally different target polynucleotides comprising an immune gene sequence to obtain a dataset of sequence reads; j) grouping the sequence reads having an identical UMI into UMI families; k) removing from the dataset UMI families with relative representation of less than 10%, e.g., is less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1%.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates an embodiment of an immuno-PETE reaction. The embodiment illustrated is a two-primer T cell receptor (TCR) primer extension target enrichment (PETE) reaction.

FIG. 2 is an image of exemplary primer extension products obtained by the immuno-PETE assay of Example 1 analyzed by agarose gel electrophoresis.

FIG. 3 is a Venn diagram demonstrating the number of clones and overlap between de-duped and de-deduped sequencing data from exemplary primer extension products obtained by the immuno-PETE assay of Example 1.

FIG. 4 illustrates an embodiment of an immuno-PETE reaction. The embodiment illustrated is a RNA or mRNA based immuno-PETE reaction.

FIG. 5 is an image of exemplary primer extension products obtained by the immuno-PETE assay of Example 3 analyzed by agarose gel electrophoresis.

FIG. 6 is a graph showing clonotyping of T cell receptor alpha and beta chains using human FACS sorted T cells (SEQ ID NO: 274-311).

FIG. 7 is a graph showing clonotyping of T cell receptor alpha and beta chains using low DNA input amounts from FFPE tissue sample cells (SEQ ID NO:312-317).

FIG. 8 is a diagram of the workflow of the immune-PETE method illustrating the steps of the first primer extension with a V-gene primer and removing the excess primer with a thermolabile exonuclease.

FIG. 9 is a diagram of the workflow of the immune-PETE method illustrating the steps of the second primer extension with a J-gene primer and a short opposite facing primer and removing the excess of both primers with a thermolabile exonuclease.

FIG. 10 is a diagram of the workflow of the immune-PETE method illustrating the steps of amplifying the primer extension product with two universal indexed primers annealing to adapter sites introduced by the V-gene primer and the J-gene primer.

FIG. 11 is an illustration of the principle of the contamination reduction method according to the invention.

FIG. 12 shows results of applying the contamination reduction method to an experimental sample.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. See, e.g., Lackie, DICTIONARY OF CELL AND MOLECULAR BIOLOGY, Elsevier (4^(th) ed. 2007); Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Lab Press (Cold Spring Harbor, NY 1989). The term “a” or “an” is intended to mean “one or more.” The term “comprise,” and variations thereof such as “comprises” and “comprising,” when preceding the recitation of a step or an element, are intended to mean that the addition of further steps or elements is optional and not excluded. Any methods, devices and materials similar or equivalent to those described herein can be used in the practice of this invention. The following definitions are provided to facilitate understanding of certain terms used frequently herein and are not meant to limit the scope of the present disclosure.

As used herein, the term “substantially all” in reference to removing substantially all of a component of a reaction mixture means removing at least 90%, 95%, 99%, or more of a component.

As used herein, the term “immune cell receptor” refers to a T cell receptor (TCR), or a B cell receptor (BCR) (i.e., antibody). The BCR can be in a membrane bound form or a secreted form.

“T cell receptor” or “TCR” refers to the antigen recognition complex of a T cell. The TCR is composed of two different protein chains (e.g., alpha and beta or gamma and delta). Each chain is composed of two extracellular domains containing a variable region (V), a joining region (J), and a constant region (C). The variable region contains hypervariable complementarity determining regions (CDRs). Beta and delta TCR chains further contain a diversity region (D) between the V and J regions. Further TCR diversity is generated by VJ (for alpha and gamma chains) and VDJ (for beta and delta chains) recombination. The terms also refer to various recombinant and heterologous forms, including soluble TCRs expressed from a heterologous system.

The B cell receptor or “BCR” refers to the secreted or membrane bound antigen recognition complex of a B cell. The BCR is composed of two different protein chains (e.g., heavy and light). Each chain contains a variable region (V), a joining region (J), and a constant region (C). The variable region contains hypervariable complementarity determining regions (CDRs). Heavy chains can further contain a diversity region (D) between the V and J regions. Further BCR diversity is generated by VJ (for light chains) and VDJ (for heavy chains) recombination as well as somatic hypermutation of recombined chains. The terms also refer to various recombinant and heterologous forms.

As used herein, the term “barcode” refers to a nucleic acid sequence that can be detected and identified. Barcodes can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more nucleotides long. Barcodes can employ error-correcting codes such that one or more errors in synthesis, replication, and/or sequencing can be corrected to identify the barcode sequence. Examples of error correcting codes and their use in barcodes and barcode identification and/or sequencing include, but are not limited to, those described in U.S. 2010/0,323,348; and U.S. Pat. No. 8,715,967. In some cases, the barcodes are designed to have a minimum number of distinct nucleotides with respect to all other barcodes of a population. The minimum number can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more. Thus, for example, a population of barcodes having a minimum number of at least five distinct nucleotides will differ at least five nucleotide positions from all other barcodes in the population.

As used herein, the term “multiplex identifier,” “MID,” and the like, refers to a barcode that identifies a source or sample. As such, all or substantially all, MID barcoded polynucleotides from a single source or sample will share an MID of the same sequence; while all, or substantially all (e.g., at least 90% or 99%), MID barcoded polynucleotides from different sources or samples will have a different MID barcode sequence. Polynucleotides from different sources or samples and having different MIDs can then be mixed and sequenced in parallel while maintaining source/sample information. Thus sequence reads can be assigned to individual samples.

As used herein, the term “universal identifier,” “universal molecular identifier,” “unique molecular identifier,” “UID,” and the like, refers to a barcode that identifies a polynucleotide to which it is attached. Typically, all, or substantially all (e.g., at least 90% or 99%), UID barcodes in a mixture of UID barcoded polynucleotides are unique.

The term “nucleic acid” or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologues, SNPs, and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).

“Polymerase” refers to an enzyme that performs template-directed synthesis of polynucleotides. A DNA polymerase can add free nucleotides only to the 3′ end of the newly forming strand. This results in elongation of the newly forming strand in a 5′-3′ direction. No known DNA polymerase is able to begin a new chain (de novo). DNA polymerase can add a nucleotide only on to a pre-existing 3′—OH group, and, therefore, needs a primer at which it can add the first nucleotide. Non-limiting examples of polymerases include prokaryotic DNA polymerases (e.g. Pol I, Pol II, Pol III, Pol IV and Pol V), eukaryotic DNA polymerase, telomerase, reverse transcriptase and RNA polymerase. Reverse transcriptase is an RNA-dependent DNA polymerase that synthesizes DNA from an RNA template. The reverse transcriptase family contain both DNA polymerase functionality and RNase H functionality, which degrades RNA base-paired to DNA. RNA polymerase is an enzyme that synthesizes RNA using DNA as a template during the process of gene transcription. RNA polymerase polymerizes ribonucleotides at the 3′-end of an RNA transcript.

In some embodiments, a polymerase from the following may be used in a polymerase-mediated primer extension, end-modification (e.g., terminal transferase, degradation, or polishing), or amplification reaction: archaea (e.g., Thermococcus litoralis (Vent, GenBank: AAA72101), Pyrococcus furiosus (Pfu, GenBank: D12983, BAA02362), Pyrococcus woesii, Pyrococcus GB-D (Deep Vent, GenBank: AAA67131), Thermococcus kodakaraensis KODI (KOD, GenBank: BD175553, BAA06142; Thermococcus sp. strain KOD (Pfx, GenBank: AAE68738)), Thermococcus gorgonarius (Tgo, Pdb: 4699806), Sulfolobus solataricus (GenBank: NC002754, P26811), Aeropyrum pernix (GenBank: BAA81109), Archaeglobus fulgidus (GenBank: 029753), Pyrobaculum aerophilum (GenBank: AAL63952), Pyrodictium occultum (GenBank: BAA07579, BAA07580), Thermococcus 9 degree Nm (GenBank: AAA88769, Q56366), Thermococcus fumicolans (GenBank: CAA93738, P74918), Thermococcus hydrothermalis (GenBank: CAC18555), Thermococcus sp. GE8 (GenBank: CAC12850), Thermococcus sp. JDF-3 (GenBank: AX135456; Wo0132887), Thermococcus sp. TY (GenBank: CAA73475), Pyrococcus abyssi(GenBank: P77916), Pyrococcus glycovorans (GenBank: CAC12849), Pyrococcus horikoshii (GenBank: NP 143776), Pyrococcus sp. GE23 (GenBank: CAA90887), Pyrococcus sp. ST700 (GenBank: CAC 12847), Thermococcus pacificus (GenBank: AX411312.1), Thermococcus zilligii (GenBank: DQ3366890), Thermococcus aggregans, Thermococcus barossi, Thermococcus celer (GenBank: DD259850.1), Thermococcus profundus (GenBank: E14137), Thermococcus siculi (GenBank: DD259857.1), Thermococcus thioreducens, Thermococcus onnurineus NA1, Sulfolobus acidocaldarium, Sulfolobus tokodaii Pyrobaculum calidifontis, Pyrobaculum islandicum (GenBank: AAF27815), Methanococcus jannaschii (GenBank: Q58295), Desulforococcus species TOK, Desulfurococcus, Pyrolobus, Pyrodictium, Staphylothermus, Vulcanisaetta, Methanococcus (GenBank: P52025) and other archaeal B polymerases, such as GenBank AAC62712, P956901, BAAA07579)), thermophilic bacteria Thermus species (e.g., flavus, ruber, thermophilus, lacteus, rubens, aquaticus), Bacillus stearothermophilus, Thermotoga maritima, Methanother musfervidus, KOD polymerase, TNA1 polymerase, Thermococcus sp. 9 degrees N-7, T4, T7, phi29, Pyrococcus furiosus, P. abyssi, T. gorgonarius, T. litoralis, T. zilligii, T. sp. GT, P. sp. GB-D, KOD, Pfu, T. gorgonarius, T. zilligii, T. litoralis and Thermococcus sp. 9N-7 polymerases.

In some embodiments, the polymerase can include a RNA polymerase from an eukaryote such as RNA polymerase I, RNA polymerase II, RNA polymerase III, RNA polymerase IV or RNA polymerase V. The polymerase can include a bacterial RNA polymerase as well as phage and viral RNA polymerases. In some aspects, the RNA polymerase can include a T7 RNA polymerase, T3 RNA polymerase, K11 RNA polymerase, K1F RNA polymerase, N4 RNA polymerase or SP6 RNA polymerase. In some embodiments, the RNA polymerase (e.g., E col/RNA polymerase) can include a wild-type, mutant or artificially engineered RNA polymerase. As used herein, “an artificially engineered RNA polymerase” consists, or comprises, of at least one amino acid substitution, deletion or insertion with respect to the wild-type or naturally occurring RNA polymerase from which the artificially engineered RNA polymerase is obtained or derived.

In some embodiments, the polymerase can include a reverse transcriptase (RT). RT is an RNA-dependent DNA polymerase that synthesizes double-stranded DNA (cDNA) from a single-stranded RNA template. The RT family contain both DNA polymerase functionality and RNase H functionality, which degrades RNA base-paired to DNA. RT's are predominately associated with retroviruses although non-retroviruses also use RT (e.g. Hepatitis B virus). In some aspects, the polymerase can include a RT from Human Immunodeficiency Virus (e.g., HIV-1), Moloney Murine Leukemia Virus (e.g., M-MLV), Human T-Lymphotrophic Virus (e.g., HTLV), Avian Myeloblastosis Virus (e.g., AMV), Rous Sarcoma Virus (e.g., RSV), SuperScript RT (e.g., SuperScript IV), or Telomerase RT (e.g., TERT). In some embodiments, the RT can include a recombinant RT (e.g., an RT having one or more amino acid substitutions, deletions or additions as compared to the corresponding wild-type or naturally occurring RT). In some aspects, the RT includes transcription of RNA fragments of various sizes (e.g., 1 kb, 5 kb, 10 kb, 15 kb, 20 kb, or more).

The term “thermostable polymerase,” refers to an enzyme that is stable to heat, is heat resistant, and retains sufficient activity to effect subsequent polynucleotide extension reactions and does not become irreversibly denatured (inactivated) when subjected to the elevated temperatures for the time necessary to effect denaturation of double-stranded nucleic acids. The heating conditions necessary for nucleic acid denaturation are well known in the art and are exemplified in, e.g., U.S. Pat. Nos. 4,683,202, 4,683,195, and 4,965,188, which are incorporated herein by reference. As used herein, a thermostable polymerase is suitable for use in a temperature cycling reaction such as the polymerase chain reaction (“PCR”), a primer extension reaction, or an end-modification (e.g., terminal transferase, degradation, or polishing) reaction. Irreversible denaturation for purposes herein refers to permanent and complete loss of enzymatic activity. For a thermostable polymerase, enzymatic activity refers to the catalysis of the combination of the nucleotides in the proper manner to form polynucleotide extension products that are complementary to a template nucleic acid strand. Thermostable DNA polymerases from thermophilic bacteria include, e.g., DNA polymerases from Thermotoga maritima, Thermus aquaticus, Thermus thermophilus, Thermus flavus, Thermus filiformis, Thermus species sps17, Thermus species Z05, Thermus caldophilus, Bacillus caldotenax, Thermotoga neopolitana, Thermosipho africanus, and other thermostable DNA polymerases disclosed above.

In some cases, the nucleic acid (e.g., DNA or RNA) polymerase may be a modified naturally occurring Type A polymerase. A further embodiment of the invention generally relates to a method wherein a modified Type A polymerase, e.g., in a primer extension, end-modification (e.g., terminal transferase, degradation, or polishing), or amplification reaction, may be selected from any species of the genus Meiothermus, Thermotoga, or Thermomicrobium. Another embodiment of the invention generally pertains to a method wherein the polymerase, e.g., in a primer extension, end-modification (e.g., terminal transferase, degradation or polishing), or amplification reaction, may be isolated from any of Thermus aquaticus (Taq), Thermus thermophilus, Thermus caldophilus, or Thermus filiformis. A further embodiment of the invention generally encompasses a method wherein the modified Type A polymerase, e.g., in a primer extension, end-modification (e.g., terminal transferase, degradation, or polishing), or amplification reaction, may be isolated from Bacillus stearothermophilus, Sphaerobacter thermophilus, Dictoglomus thermophilum, or Escherichia coli. In another embodiment, the invention generally relates to a method wherein the modified Type A polymerase, e.g., in a primer extension, end-modification (e.g., terminal transferase, degradation, or polishing), or amplification reaction, may be a mutant Tag-E507K polymerase. Another embodiment of the invention generally pertains to a method wherein a thermostable polymerase may be used to effect amplification of the target nucleic acid.

As used herein the term “primer” refers to an oligonucleotide that binds to a specific region of a single stranded template nucleic acid molecule and initiates nucleic acid synthesis via a polymerase-mediated enzymatic reaction, extending from the 3′ end of the primer and complementary to the sequence of the template molecule. PCR amplification primers can be referred to as ‘forward’ and ‘reverse’ primers, one of which is complementary to a nucleic acid strand and the other of which is complementary to the complement of that strand. Typically, a primer comprises fewer than about 100 nucleotides and preferably comprises fewer than about 30 nucleotides. Exemplary primers range from about 5 to about 25 nucleotides. Primers can comprise, for example, RNA and/or DNA bases, as well as non-naturally-occurring bases. The directionality of the newly forming strand (the daughter strand) is opposite to the direction in which DNA polymerase moves along the template strand.

As used herein, the term “universal primer” and “universal primers” refers to a primer that can hybridize to and support amplification of target polynucleotides having a shared complementary universal primer binding site. Similar, the term “universal primer pair” refers to a forward and reverse primer pair that can hybridize to and support PCR amplification of target polynucleotides having shared complementary forward and reverse universal primer binding sites. Such universal primer(s) and universal primer binding site(s) can allow single or double-primer mediated universal amplification (e.g., universal PCR) of target polynucleotide regions of interest.

As used herein the term “sample” refers to any biological sample that comprises nucleic acid molecules, typically comprising DNA and/or RNA. Samples may be tissues, cells or extracts thereof, or may be purified samples of nucleic acid molecules. Use of the term “sample” does not necessarily imply the presence of target sequence within nucleic acid molecules present in the sample. In some cases, the “sample” comprises immune cells (e.g., B cells and/or T cells), or a fraction thereof (e.g., a fraction enriched in genomic DNA, total RNA, or mRNA). In some embodiments, a sample can comprise a FACS sorted population of cells (such as human T cells) or a fixed formalin paraffin embedded (FFPE) tissue sample.

As used herein, the phrase “stringent hybridization conditions” refers to conditions under which a primer/probe will hybridize to its target, typically in a complex mixture of nucleic acids, but not to other nucleic acid sequences present in the complex mixture. Stringent conditions are sequence-dependent and will be different under different circumstances. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, high stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength pH. Low stringency conditions are generally selected to be about 15-30° C. below the T_(m). The T_(m) is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the primers/probes complementary to the target hybridize to the target sequence at equilibrium. Stringent conditions include those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short primers/probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long primers/probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.

DETAILED DESCRIPTION OF THE INVENTION I. Introduction

The present invention provides a primer extension target enrichment (PETE) method that includes two flanking primers and compositions for performing and using the flanking primer PETE (FP-PETE) method. The use of two flanking primers increases the stringency of the enrichment step as compared to methods that require only a single primer or single bait for enrichment of each structurally distinct target polynucleotide. Thus, in some cases, the FP-PETE method provides improved or synergistic target enrichment in comparison to other target enrichment methods such as, e.g., single primer extension target enrichment methods.

Moreover, in contrast to multiplex PCR based methods in which multiple first and second amplification primers are in the same reaction mixture at the same time, the FP-PETE method can include a step of removing un-extended first primers before introducing second primers into a reaction mixture. Thus, in some cases, the method can reduce or eliminate competition between first and second primers. As such, in some cases, the first or second primers, or both can be used at significantly higher concentrations in the FP-PETE reaction mixture as compared to, e.g., multiplex PCR based methods. Additionally, or alternatively, an increased number of first or second primers can be used in the FP-PETE reaction mixture as compared to, e.g., multiplex PCR based methods.

The use of a large number of first or second primers, a high concentration of first or second primers, or a combination thereof, can provide improved enrichment for, e.g., high-throughput sequencing sample workflows in which a large number of different polynucleotide sequences are targeted and flanking hybridization sequences for the target sequences are known. Such high-throughput sequencing sample workflows include, but are not limited to, immune repertoire profiling workflows in which B cell receptor (BCR) or T cell receptor (TCR) sequences are enriched from a sample, sequenced, and analyzed. Flanking primer extension target enrichment methods for immune repertoire profiling workflows is termed “immuno-PETE.”

Hybridization conditions including those exemplified herein are readily determinable by one of ordinary skill in the art, and can include calculating primer/probe length, salt concentration, and preferential temperature to limit non-specific hybridization. In general, longer primers/probes require higher temperatures for correct annealing, while shorter primer/probes require lower temperatures. Hybridization generally depends on the ability of denatured DNA to anneal complementary nucleic acid sequences (e.g., primer/probes) present in an environment (e.g., a reaction mixture) below their melting temperature. The higher the degree of homology between a primer/probe and denatured DNA, the higher the annealing temperature can be while minimizing non-specific hybridization. Accordingly, higher relative annealing temperatures tend to make the reaction conditions more “stringent”, while lower annealing temperatures make the reaction conditions less so. Additional details and explanations of hybridization stringency can be found for example in Ausubel et al., (Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995)).

In some embodiments, the invention is a primer extension targeted gene enrichment assay designed to specifically enrich and amplify human T-cell receptor (TCR) loci and B-cell receptor (BCR) loci from genomic DNA, and result in unbiased and quantitative TCR and BCR repertoire information upon next-generation sequencing analysis. In some embodiments, the invention is a primer extension target enrichment assay optimized for the human TCR-beta locus (TRB) as well as BCR-heavy chain locus (IGH). In some embodiments, the invention is a primer extension target enrichment assay optimized for Illumina MiSeq or NextSeq next-generation sequencing platforms.

In one aspect, the present invention provides first or second primers (e.g., SEQ ID NOs:1-121, 122-204, 205-213, etc.) that selectively hybridize to certain target polynucleotides. The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule (e.g., a target polynucleoctide) to a particular nucleotide sequence (e.g., a primer or probe comprising SEQ ID NOS:1-213) under stringent hybridization conditions when the target polynucleotide is present in a reaction mixture (e.g., total RNA, mRNA, cDNA or gDNA).

In one embodiment, the first or second primers described herein are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to the target polynucleotides. In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to the target polynucleotides. In another embodiment, the first or second primers are complementary across their full-length to the target polynucleotides.

In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene. In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene. In another embodiment, the first or second primers are complementary across their full-length to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene.

In yet another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to an immune cell receptor J gene region. In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to an immune cell receptor J gene region. In another embodiment, the first or second primers are complementary across their full-length to an immune cell receptor J gene region.

In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to an immune cell receptor C gene region. In another embodiment, the first or second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to an immune cell receptor C gene region. In another embodiment, the first or second primers are complementary across their full-length to an immune cell receptor C gene region.

In some embodiments, genomic DNA or cDNA comprising target polynucleotides of the invention can be identified under stringent hybridization conditions using the primer/probes sequences disclosed here (e.g., comprising any one or more of SEQ ID NOS:1-213). The following is an exemplary set of hybridization conditions performed on a thermocycler and is not limiting: a) denaturation of sample containing target polynucleotides at 98° C. for 2 minutes; b) hybridization or primers/probes at 60° C. for 20 minutes; c) extension of primers/probes using polymerase at 65° C. for 2 minutes; d) addition of Exonuclease I to reaction mixture at 37° C. for 10 minutes, increase temperature to 80° C. for a further 10 minutes, hold at 4° C.

In one embodiment, target polynucleotides that selectively hybridize to any one of the primer/probe sequences disclosed herein (e.g. SEQ ID NOS: 1-213) can be of any length, e.g., at least 10, 15, 20, 25, 30, 50, 100, 200, 500 or more nucleotides or having fewer than 500, 200, 100, or 50 nucleotides, etc.).

In one embodiment, a first primer is hybridized to a region of a target immune cell receptor polynucleotide that is 3′ to a region of interest or at a 3′ end of a region of interest. For example, the region of interest can include at least a portion of the immune cell receptor V region, at least a portion of the C region, the diversity (D) region if present, and at least a portion of the J region. In some cases, the first primer hybridizes to a framework region (e.g., a framework 1, framework 2, or framework 3 region) of the immune cell receptor V region. In some cases, the first primer hybridizes to the immune cell receptor C region (e.g., comprising a C-segment primer). The first primer can then be extended by a polymerase in a first extension reaction. Un-extended first primers and other single-stranded nucleic acid (e.g., denatured genomic DNA) can then be removed, e.g., by single-stranded DNA exonuclease digestion. In a second reaction, a second primer hybridizes to a region of the extended first primer that is 3′ to the region of interest or at a 3′ end of a region of interest. Thus, the first and second primers flank the region of interest when hybridized to their respective targets. In some cases, the second primer hybridizes to a J-gene region of the extended first primer. In some cases, the second primer hybridizes to a V-gene region of the extended first primer. In some cases, the second primer hybridizes to a C gene region of the extended first primer. The second primer can then be extended by a polymerase in a second extension reaction.

Alternatively, a first primer can be hybridized to a J-gene region of a target immune cell receptor polynucleotide that is 3′ to a region of interest or at a 3′ end of a region of interest. The hybridized first primer can then be extended by a polymerase. Un-extended first primers and other single-stranded nucleic acid (e.g., denatured genomic DNA) can then be removed, e.g., by single-stranded DNA exonuclease digestion. In a second reaction, a second primer can be hybridized to a framework region of the extended first primer and extended with a polymerase.

In one embodiment, complementary DNA (cDNA) can be prepared from RNA or mRNA for use in the PETE methods described herein. In one aspect, cDNA is prepared from total RNA or mRNA isolated and/or purified from a cell, cell lysate, sample or tissue. In one embodiment, RNA can include total RNA obtained using RNA isolation and/or extraction methods known in the art (e.g., Molecular Cloning: A Laboratory Manual, 4^(th) Edition, Vol. 1, Chapter 6 (2012) incorporated herein by reference for all purposes; RNeasy Mini Kit (Catalog Number: 74104), Qiagen, Germantown, MD). In another embodiment, cDNA can be synthesized from total RNA or mRNA transcripts using commercially available kits (for example, SuperScript III™ Reverse Transcriptase (Catalog Number: 18080093) or SuperScript® VILO™ cDNA Synthesis Kit (Catalog Number: 11754050), ThermoFisher Scientific, Waltham, MA). In another embodiment, cDNA can be prepared from total RNA or mRNA transcripts obtained from whole blood, peripheral blood mononuclear cell (PBMC), sorted lymphocytes, lymphocyte culture, fresh or fresh-frozen tumor tissue or formalin-fixed paraffin embedded (FFPE) tissue (for example, RNeasy FFPE kit, Qiagen, Germantown, MD). In one aspect, cDNA synthesis can be initiated at or near the 3′ termini of the mRNA transcript and terminates at or near the 5′ end of the mRNA so as to generate “full-length” cDNA molecules.

In one embodiment, mRNA purified from a sample (e.g., cell, cell lysate or tissue) can be primed with an oligo-dT primer (e.g., a poly-T primer), random primer mixture (for example, a mixture or random hexamers, heptamers, octamers, nanomers, etc.,) or one or more isotype-specific immune receptor Constant-region (C-segment) primers (e.g., comprising SEQ ID NOS:205-213 of Table 6) under hybridization conditions sufficient to initiate cDNA synthesis (see FIG. 4 ). In one aspect, the oligo-dT primer facilitates the 3′ end of the mRNA's in the sample being represented in the resulting cDNA molecules. In another aspect, the one or more isotype-specific immune receptor C-segment primers allows for hybridization of the C-segment primer to a complementary sequence among the one or more mRNA transcripts present in the sample. In one embodiment, the resulting cDNA molecules can be used in one or more of the PETE assays as described herein to produce one or more primer extension products that can be used to identify immune receptor isotypes in the sample. Accordingly, RNA or mRNA molecules of the sample can undergo first, and preferably, second strand synthesis to produce double-stranded cDNA molecules. In one embodiment, cDNA is prepared using an oligo-dT primer as set forth in this paragraph. In another embodiment, cDNA is prepared using a random primer mixture of hexamers, heptamers, octamers, nanomers, etc., as set forth in this paragraph. In another embodiment, cDNA is prepared using at least one isotype-specific immune receptor C-segment primer. In another embodiment, cDNA can be prepared using one or more C-gene region primers. For example Glanville et al., (PNAS, (2009) 106.48, 20216-21) discloses using a human heavy chain constant region primer, human kappa constant region primer and human lambda constraint region primer to prepare cDNA from total RNA and/or mRNA from human samples. In yet another embodiment, cDNA is prepared using at least one of the isotype-specific immune receptor C-segment primers set forth in SEQ ID NOS:205-213.

Once prepared, the synthesized cDNA can be purified by any method known in the art (e.g., Solid Phase Reversible Immobilization (SPRI) paramagnetic beads or AMPure paramagnetic beads (Beckman Coulter, Brea, CA), filtration or centrifugation columns (e.g. RNeasy Mini Kit (Catalog Number: 74104), Qiagen, Germantown, MD). The purified cDNA can then serve as a template for any of the methods described herein. In one embodiment, a plurality of V gene specific primers (e.g., comprising SEQ ID NOS:1-121) can be used in the first round of primer extension (gPE extension), followed by a second round of extension using one or more C-segment primers (e.g., comprising SEQ ID NOS:205-213, see Table 6). Alternatively, cDNA prepared as described herein can be used as the starting template for the PETE assays described herein (e.g., Example 1), where a plurality of V gene specific primers (e.g., comprising SEQ ID NOS:1-121) can be used in the first round of primer extension (gPE extension), followed by a second round of extension (PE2 extension) using a plurality of J-gene specific primers (e.g., comprising SEQ ID NOS:122-204).

II. Compositions

Described herein are compositions for performing immuno-PETE. Such compositions can include one or more, or all, of the following: primers, primer sets, polymerase extension products of such primers or primer sets (e.g., hybridized to a target polynucleotide), target polynucleotides (e.g., single-stranded target polynucleotides), reaction mixtures, DNA-dependent DNA polymerases, RNA-dependent DNA polymerases, single-stranded DNA exonucleases, nucleotides, buffers, salts, and the like.

In one embodiment, a composition containing a plurality of first primers is provided. In some cases, the plurality of first primers are immune cell receptor gene specific primers. The plurality of immune cell receptor gene specific primers can be configured to hybridize to, and thus enrich in a polymerase-mediated extension step, a plurality of target polynucleotides in a sample that encode immune cell receptor genes. The first primers can include a 5′-terminal phosphate (“[5′-Phos]”). The 5′-terminal phosphate can allow for ligation of the 5′ end of the first primer, or a polymerase extension product thereof, to a 3′-OH of an adjacent polynucleotide.

The first primers can include a [SPLINT] region. The [SPLINT] region can include an adapter hybridization site of at least 2 nucleotides in length. In some cases, the adapter hybridization site is at least 4 nucleotides in length, at least 6 nucleotides in length, at least 8 nucleotides in length, from 2 to 10 nucleotides in length, or from 2 to 8 nucleotides in length. The [SPLINT] region can be complementary to a single-stranded 5′ overhang region of a double-stranded adapter, such that when the single-stranded 5′ overhang region of the double-stranded adapter hybridizes to the [SPLINT] region, a 3′-OH of the adapter can be ligated to the [5′-Phos] of the first primer or a polymerase extension product thereof. In some embodiments, [SPLINT] comprises or consists of 6 consecutive nucleotides that are complementary to a single-stranded 5′ overhang region of a double-stranded adapter. In some embodiments, [SPLINT] comprises or consists of the sequence CGA TCT.

The first primers can include a [BARCODE] region that is or contains a barcode. The [BARCODE] region can be or contain a UID, an MID, or a combination thereof. In some cases, the [BARCODE] region comprises a UID. The [BARCODE] region can be any length from 2 to about 50 or more nucleotides. For UID barcodes, generally, the barcode length and composition is selected to encode more sequences than there are unique target polynucleotides to barcode. As such, for immune repertoire profiling, where estimates of diversity are generally significantly greater than 103 and each unique sequence can be represented in a sample multiple times, the UID barcode can be at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 nucleotides in length. For example, in some cases the barcode can be from 6 to 16 nucleotides in length, from 8 to 14 nucleotides in length, or from 10 to 13 nucleotides in length. In some embodiments, the barcode is 13 nucleotides in length. In some cases, the barcode comprises nucleotides selected from the group consisting of N and W. In an exemplary embodiment, the barcode has a sequence of WNN NNN WNN NNN W (SEQ ID NO:524).

The first primers can include a [FW] region. The [FW] region can be or contain a structurally distinct sequence that specifically hybridizes to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene region of an immune cell receptor (TCR or BCR) encoding target polynucleotide, wherein upon hybridization to the V gene region of an immune cell receptor encoding target polynucleotide, the first primer can be extended in the direction of the J gene region of the immune cell receptor encoding target polynucleotide. In some embodiments, the [FW] region hybridizes to a framework 1, framework 2, or framework 3 region of an TCR encoding target polynucleotide. In some embodiments, the [FW] region hybridizes to a framework 1, framework 2, or framework 3 region of a BCR encoding target polynucleotide. First primers containing a [FW] region can be used in an immuno-PETE method with second primers that hybridize to the J gene region of an immune cell receptor encoding target polynucleotide. In some embodiments, the first primers include the following regions: [5′-Phos], [SPLINT], [BARCODE], and [FW]. In some embodiments, the first primers include the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [FW].

Alternatively, the first primers can include a J-specific region ([J]) that specifically hybridizes to a J gene region of an immune cell receptor encoding target polynucleotide, wherein upon hybridization to the J gene region of an immune cell receptor (TCR or BCR) encoding target polynucleotide, the first primer can be extended in the direction of the V gene region of the immune cell receptor encoding target polynucleotide. In some embodiments, the [J] region hybridizes to a J gene region of a TCR encoding target polynucleotide. In some embodiments, the [J] region hybridizes to a J gene region of a BCR encoding target polynucleotide. First primers containing a region [J] can be used in an immuno-PETE method with second primers that hybridize to the framework 1, framework 2, or framework 3 region of an immune cell receptor encoding target polynucleotide. In some embodiments, the first primers include the following regions: [5′-Phos], [SPLINT], [BARCODE], and [J]. In some embodiments, the first primers include the following regions from 5′ to 3′: [5′-Phos], [SPLINT], [BARCODE], and [J]. In another embodiment, the first primers can include a Constant-specific region ([C]) that specifically hybridizes to a C gene region of an immune cell receptor encoding target polynucleotide, wherein upon hybridization to the C gene region of an immune cell receptor (TCR or BCR) encoding target polynucleotide, the first primer can be extended in a 3′ direction, through the C gene region of the immune cell receptor encoding target polynucleotide. In some embodiments, the [C] region hybridizes to a C gene region of a TCR encoding target polynucleotide. In some embodiments, the [C] region hybridizes to a C gene region of a BCR encoding target polynucleotide. In some embodiments, first primers containing a C-region [C] can be used in an immuno-PETE method with second primers that hybridize to the V-specific region ([V]) that specifically hybridizes to a V gene region of an immune cell receptor encoding target polynucleotide. In some embodiments, the first primers include the following regions: [5′-Phos], [SPLINT], [BARCODE], and [C]. In some embodiments, where the sample includes purified mRNA or total RNA, the first primers can include a C-segment primer that is complementary to, and hybridizes under hybridization conditions with a C gene region of an immune cell receptor encoding polynucleotide, or a complement thereof.

In one aspect, the present invention provides first primers (e.g., SEQ ID NOs: 205-213) that can selectively hybridize to certain target polynucleotides. The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule (e.g., a target polynucleoctide) to a particular nucleotide sequence (e.g., a primer or probe comprising SEQ ID NOS: 205-213) under stringent hybridization conditions when the target polynucleotide is present in a reaction mixture (e.g., total RNA, mRNA, cDNA or gDNA).

As described herein, target polynucleotides encoding a TCR β-chain or 6-chain can contain a D region that is positioned between a V region and a J region, whereas target polynucleotides encoding a TCR α-chain or γ-chain can lack a D region, such that the V region and J region are adjacent. Similarly, target polynucleotides encoding a BCR heavy chain can contain a D region that is positioned between a V region and a J region, whereas target polynucleotides encoding a BCR light chain can lack a D region, such that the V region and J region are adjacent.

As such, first primer extension products of first primers containing an [FW] region that are templated by a TCR β-chain or 6-chain or BCR heavy chain can, e.g., contain a VDJ region, or a portion of the V region, a D region, and a J region. Similarly, first primer extension products of first primers containing an [FW] region that are templated by a TCR α-chain or γ-chain or a BCR light chain can lack a D region, and thus contain a V region or portion thereof adjacent to a J region. Alternatively, first primer extension products of first primers containing a [J] region that are templated by a TCR β-chain or δ-chain or BCR heavy chain can, e.g., contain a VDJ region, or a portion of the J region, a D region, and a V region. Similarly, first primer extension products of first primers containing a [J] region that are templated by a TCR α-chain or γ-chain or a BCR light chain can lack a D region, and thus contain a J region or portion thereof adjacent to a V region.

In some embodiments, the plurality of first primers contains at least 2, at least 5, at least 10, at least 25, at least 50, at least 100, or all of the primers set forth in Table 1 (SEQ ID Nos: 1-121). In one embodiment, the plurality of first primers contains at least 1 of the primers set forth in SEQ ID Nos: 1-121. In some embodiments, the plurality of first primers contains at least 2, at least 5, at least 10, or all of the primers set forth in SEQ ID NOS: 205-213. In one embodiment, the plurality of first primers contains at least 1 of the primers set forth in SEQ ID NOS: 205-213. In one embodiment, the plurality of first primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to an immune cell receptor C gene region. In another embodiment, the first primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to an immune cell receptor C gene region. In another embodiment, the first primers are complementary across their full-length to an immune cell receptor C gene region.

TABLE 1 SEQ ID NO: 1. [5′-Phos]-[SPLINT]-[BARCODE]-GA ATG CCC TGA CAG CTC TCG CTT ATA SEQ ID NO: 2. [5′-Phos]-[SPLINT]-[BARCODE]-CT CAG AGA AGT CTG AAA TAT TCG ATG ATC AAT TCT CAG TTG SEQ ID NO: 3. [5′-Phos]-[SPLINT]-[BARCODE]-CC AAA TCG MTT CTC ACC TAA ATC TCC AGA CAA AG SEQ ID NO: 4. [5′-Phos]-[SPLINT]-[BARCODE]-CA CCT GAC TCT CCA GAC AAA GCT CAT SEQ ID NO: 5. [5′-Phos]-[SPLINT]-[BARCODE]-CC TGA ATG CCC CAA CAG CTC TC SEQ ID NO: 6. [5′-Phos]-[SPLINT]-[BARCODE]-GA TTC TCA GGG CGC CAG TTC TCT A SEQ ID NO: 7. [5′-Phos]-[SPLINT]-[BARCODE]-CC TAA TTG ATT CTC AGC TCA CCA CGT CCA TA SEQ ID NO: 8. [5′-Phos]-[SPLINT]-[BARCODE]-TC AGG GCG CCA GTT CCA TG SEQ ID NO: 9. [5′-Phos]-[SPLINT]-[BARCODE]-TC CTA GAT TCT CAG GTC TCC AGT TCC CTA SEQ ID NO: 10. [5′-Phos]-[SPLINT]-[BARCODE]-GA GGA AAC TTC CCT GAT CGA TTC TCA GC SEQ ID NO: 11. [5′-Phos]-[SPLINT]-[BARCODE]-CA ACT TCC CTG ATC GAT TCT CAG GTC A SEQ ID NO: 12. [5′-Phos]-[SPLINT]-[BARCODE]-AG GAA ACT TCC CTG ATC AAT TCT CAG GTC A SEQ ID NO: 13. [5′-Phos]-[SPLINT]-[BARCODE]-GG AAA CTT CCC TCC TAG ATT TTC AGG TCG SEQ ID NO: 14. [5′-Phos]-[SPLINT]-[BARCODE]-CC CCA ATG GCT ACA ATG TCT CCA GAT T SEQ ID NO: 15. [5′-Phos]-[SPLINT]-[BARCODE]-GG AGA GGT CCC TGA TGG CTA CAA SEQ ID NO: 16. [5′-Phos]-[SPLINT]-[BARCODE]-TC CCT GAT GGT TAT AGT GTC TCC AGA GC SEQ ID NO: 17. [5′-Phos]-[SPLINT]-[BARCODE]-GG AGA AGT CCC CAA TGG CTA CAA TGT C SEQ ID NO: 18. [5′-Phos]-[SPLINT]-[BARCODE]-AA AGG AGA AGT CCC GAA TGG CTA CAA SEQ ID NO: 19. [5′-Phos]-[SPLINT]-[BARCODE]-GT TCC CAA TGG CTA CAA TGT CTC CAG ATC SEQ ID NO: 20. [5′-Phos]-[SPLINT]-[BARCODE]-GA AGT CCC CAA TGG CTA CAA TGT CTC TAG ATT SEQ ID NO: 21. [5′-Phos]-[SPLINT]-[BARCODE]-GA GAA GTC CCC GAT GGC TAC AAT GTA SEQ ID NO: 22. [5′-Phos]-[SPLINT]-[BARCODE]-GT GAT CGG TTC TCT GCA CAG AGG T SEQ ID NO: 23. [5′-Phos]-[SPLINT]-[BARCODE]-CG CTT CTC TGC AGA GAG GAC TGG SEQ ID NO: 24. [5′-Phos]-[SPLINT]-[BARCODE]-GG TTC TTT GCA GTC AGG CCT GA SEQ ID NO: 25. [5′-Phos]-[SPLINT]-[BARCODE]-CA GTG GTC GGT TCT CTG CAG AG SEQ ID NO: 26. [5′-Phos]-[SPLINT]-[BARCODE]-GC TCA GTG ATC AAT TCT CCA CAG AGA GGT SEQ ID NO: 27. [5′-Phos]-[SPLINT]-[BARCODE]-TT CTC TGC AGA GAG GCC TGA GG SEQ ID NO: 28. [5′-Phos]-[SPLINT]-[BARCODE]-CC CAG TGA TCG CTT CTT TGC AGA AA SEQ ID NO: 29. [5′-Phos]-[SPLINT]-[BARCODE]-CT GCA GAG AGG CCT AAG GGA TCT SEQ ID NO: 30. [5′-Phos]-[SPLINT]-[BARCODE]-GA AGG GTA CAA TGT CTC TGG AAA CAA ACT CAA G SEQ ID NO: 31. [5′-Phos]-[SPLINT]-[BARCODE]-GG GGT ACT GTG TTT CTT GAA ACA AGC TTG AG SEQ ID NO: 32. [5′-Phos]-[SPLINT]-[BARCODE]-CA GTT CCC TGA CTT GCA CTC TGA ACT AAA C SEQ ID NO: 33. [5′-Phos]-[SPLINT]-[BARCODE]-AC TAA CAA AGG AGA AGT CTC AGA TGG CTA CAG SEQ ID NO: 34. [5′-Phos]-[SPLINT]-[BARCODE]-AG ATA AAG GAG AAG TCC CCG ATG GCT A SEQ ID NO: 35. [5′-Phos]-[SPLINT]-[BARCODE]-GA TAC TGA CAA AGG AGA AGT CTC AGA TGG CTA TAG SEQ ID NO: 36. [5′-Phos]-[SPLINT]-[BARCODE]-CT AAG GAT CGA TTT TCT GCA GAG AGG CTC SEQ ID NO: 37. [5′-Phos]-[SPLINT]-[BARCODE]-TT GAT TCT CAG CAC AGA TGC CTG ATG T SEQ ID NO: 38. [5′-Phos]-[SPLINT]-[BARCODE]-AT TCT CAG CTG AGA GGC CTG ATG G SEQ ID NO: 39. [5′-Phos]-[SPLINT]-[BARCODE]-GG ATC GAT TCT CAG CTA AGA TGC CTA ATG C SEQ ID NO: 40. [5′-Phos]-[SPLINT]-[BARCODE]-CT CAG CAG AGA TGC CTG ATG CAA CTT TA SEQ ID NO: 41. [5′-Phos]-[SPLINT]-[BARCODE]-CT GAT CGA TTC TCA GCT CAA CAG TTC AGT SEQ ID NO: 42. [5′-Phos]-[SPLINT]-[BARCODE]-TA GCT GAA AGG ACT GGA GGG ACG TAT SEQ ID NO: 43. [5′-Phos]-[SPLINT]-[BARCODE]-CC AGG AGG CCG AAC ACT TCT TTC T SEQ ID NO: 44. [5′-Phos]-[SPLINT]-[BARCODE]-GC TAA GTG CCT CCC AAA TTC ACC CT SEQ ID NO: 45. [5′-Phos]-[SPLINT]-[BARCODE]-CA CAG CTG AAA GAC CTA ACG GAA CGT SEQ ID NO: 46. [5′-Phos]-[SPLINT]-[BARCODE]-CT GCT GAA TTT CCC AAA GAG GGC C SEQ ID NO: 47. [5′-Phos]-[SPLINT]-[BARCODE]-AG GGT ACA GCG TCT CTC GGG SEQ ID NO: 48. [5′-Phos]-[SPLINT]-[BARCODE]-GC CTG ACC TTG TCC ACT CTG ACA SEQ ID NO: 49. [5′-Phos]-[SPLINT]-[BARCODE]-AT GAG CGA TTT TTA GCC CAA TGC TCC A SEQ ID NO: 50. [5′-Phos]-[SPLINT]-[BARCODE]-TG AAG GCT ACG TGT CTG CCA AGA G SEQ ID NO: 51. [5′-Phos]-[SPLINT]-[BARCODE]-CT CAT CTC AAT GCC CCA AGA ACG C SEQ ID NO: 52. [5′-Phos]-[SPLINT]-[BARCODE]-AG ATC TCT GAT GGA TAC AGT GTC TCT CGA CA SEQ ID NO: 53. [5′-Phos]-[SPLINT]-[BARCODE]-AG ATC TTT CCT CTG AGT CAA CAG TCT CCA GAA TA SEQ ID NO: 54. [5′-Phos]-[SPLINT]-[BARCODE]-CA CTG AAA AAG GAG ATA TCT CTG AGG GGT ATC ATG SEQ ID NO: 55. [5′-Phos]-[SPLINT]-[BARCODE]-GT TCC TGA AGG GTA CAA AGT CTC TCG AAA AG SEQ ID NO: 56. [5′-Phos]-[SPLINT]-[BARCODE]-CT GAG GGG TAC AGT GTC TCT AGA GAG A SEQ ID NO: 57. [5′-Phos]-[SPLINT]-[BARCODE]-AG CCG CCC AAA CCT AAC ATT CTC AA SEQ ID NO: 58. [5′-Phos]-[SPLINT]-[BARCODE]-CC CAG GAC CGG CAG TTC A SEQ ID NO: 59. [5′-Phos]-[SPLINT]-[BARCODE]-TT GAT TAG AGA CAT ATC CCT ATT GAA AAT ATT TCC TGG CA SEQ ID NO: 60. [5′-Phos]-[SPLINT]-[BARCODE]-AG ATG CCC TGA GTC AGC ATA GTC ATT CTA AC SEQ ID NO: 61. [5′-Phos]-[SPLINT]-[BARCODE]-GG AGG GGA AGG CCC CAC AGC GTC TTC SEQ ID NO: 62. [5′-Phos]-[SPLINT]-[BARCODE]-TG AAG TCA TAC AGT TCC TGG TGT CCA T SEQ ID NO: 63. [5′-Phos]-[SPLINT]-[BARCODE]-CC AAA TCA GGC TTT GGA GCA CCT GAT CT SEQ ID NO: 64. [5′-Phos]-[SPLINT]-[BARCODE]-CC AAA CAA AGG CTT AGA ATA TTT ATT ACA TGT C SEQ ID NO: 65. [5′-Phos]-[SPLINT]-[BARCODE]-CC AGG TCC CTG AGG CAC TCC ACC AGC T SEQ ID NO: 66. [5′-Phos]-[SPLINT]-[BARCODE]-CT GAA TCT AAA TTA TGA GCC ATC TGA CA SEQ ID NO: 67. [5′-Phos]-[SPLINT]-[BARCODE]-TC ATT CCT TAG TCG CTC TGA TAG TTA TGG TTA SEQ ID NO: 68. [5′-Phos]-[SPLINT]-[BARCODE]-CA TTC CTT AGT CGG TCT AAA GGG TAC AGT TA SEQ ID NO: 69. [5′-Phos]-[SPLINT]-[BARCODE]-AC AAC ATG ACC TAT GAA CGG TTC TCT TCA TC SEQ ID NO: 70. [5′-Phos]-[SPLINT]-[BARCODE]-CT GAA TTT AAC AAG AGC CAA ACC TCC TTC CA SEQ ID NO: 71. [5′-Phos]-[SPLINT]-[BARCODE]-CC GAC AGA AAG TCC AGC ACT CTG AG SEQ ID NO: 72. [5′-Phos]-[SPLINT]-[BARCODE]-CA CTG TTC TAT TGA ATA AAA AGG ATA AAC ATC TGT C SEQ ID NO: 73. [5′-Phos]-[SPLINT]-[BARCODE]-GT CAC CTT TGA TAC CAC CCT TAA ACA GAG TTT SEQ ID NO: 74. [5′-Phos]-[SPLINT]-[BARCODE]-AG ACT AAA TGC TAC ATT ACT GAA GAA TGG AAG CAG SEQ ID NO: 75. [5′-Phos]-[SPLINT]-[BARCODE]-TG AGG CTG AAT TTA TAA AGA GTA AAT TCT CCT TTA A SEQ ID NO: 76. [5′-Phos]-[SPLINT]-[BARCODE]-GC TGA ATT TAA GAA GAG TGA AAC CTC CTT CCA SEQ ID NO: 77. [5′-Phos]-[SPLINT]-[BARCODE]-GG CTG AAT TTA AGA GGA GTC AAT CTT CCT TCA A SEQ ID NO: 78. [5′-Phos]-[SPLINT]-[BARCODE]-GA CAC TTA TCA CTT CCC CAA TCA ATA CCC C SEQ ID NO: 79. [5′-Phos]-[SPLINT]-[BARCODE]-GG CTG AAT TTA ACA AGA GTC AAA CTT CCT TCC A SEQ ID NO: 80. [5′-Phos]-[SPLINT]-[BARCODE]-GC TGA ATT TAA GAA GAG CGA AAC CTC CTT CTA SEQ ID NO: 81. [5′-Phos]-[SPLINT]-[BARCODE]-CC ATG TAC CGT AAA GAA ACC ACT TCT TTC CA SEQ ID NO: 82. [5′-Phos]-[SPLINT]-[BARCODE]-CC ACA TAC CGT AAA GAA ACC ACT TCT TTC CA SEQ ID NO: 83. [5′-Phos]-[SPLINT]-[BARCODE]-TG GAT GCA GAC ACA AAG CAA AGC TC SEQ ID NO: 84. [5′-Phos]-[SPLINT]-[BARCODE]-TA AAG AAC TGC TTG GAA AAG AAA AAT TTT ATA GTG T SEQ ID NO: 85. [5′-Phos]-[SPLINT]-[BARCODE]-AC AGC TCA ATA GAG CCA GCC AGT ATA TTT C SEQ ID NO: 86. [5′-Phos]-[SPLINT]-[BARCODE]-CA GCT CAA TAA AGC CAG CCA GTA TGT TTC SEQ ID NO: 87. [5′-Phos]-[SPLINT]-[BARCODE]-GC ACA GGT CGA TAA ATC CAG CAA GTA TAT CTC SEQ ID NO: 88. [5′-Phos]-[SPLINT]-[BARCODE]-CT GTT ACA TTG AAC AAG ACA GCC AAA CAT TTC TC SEQ ID NO: 89. [5′-Phos]-[SPLINT]-[BARCODE]-CA CCG TTT TAT TGA ATA AGA CAG TGA AAC ATC TCT C SEQ ID NO: 90. [5′-Phos]-[SPLINT]-[BARCODE]-CC AGA AGG CAA GAA AAT CCG CCA A SEQ ID NO: 91. [5′-Phos]-[SPLINT]-[BARCODE]-AG AAG CGC TTG GAA AAG AGA AGT TTT ATA GTG T SEQ ID NO: 92. [5′-Phos]-[SPLINT]-[BARCODE]-TG ACC TTA ACA AAG GCG AGA CAT CTT TCC A SEQ ID NO: 93. [5′-Phos]-[SPLINT]-[BARCODE]-CG CTT GAC ACT TCC AAG AAA AGC AGT TC SEQ ID NO: 94. [5′-Phos]-[SPLINT]-[BARCODE]-CA GTC CTA TCA AGA GTG ACA GTT CCT TCC A SEQ ID NO: 95. [5′-Phos]-[SPLINT]-[BARCODE]-GA ACT TCC AGA AAT CCA CCA GTT CCT TCA A SEQ ID NO: 96. [5′-Phos]-[SPLINT]-[BARCODE]-GC TAA AAG CCA CAT TAA CAA AGA AGG AAA GCT T SEQ ID NO: 97. [5′-Phos]-[SPLINT]-[BARCODE]-CT CGC TGG ATA AAT CAT CAG GAC GTA GTA C SEQ ID NO: 98. [5′-Phos]-[SPLINT]-[BARCODE]-TC GCT ACG GAA CGC TAC AGC TT SEQ ID NO: 99. [5′-Phos]-[SPLINT]-[BARCODE]-CT CCT TCA ATA AAA GTG CCA AGC AGT TCT C SEQ ID NO: 100. [5′-Phos]-[SPLINT]-[BARCODE]-CA CTC TTA ATA CCA AGG AGG GTT ACA GCT A SEQ ID NO: 101. [5′-Phos]-[SPLINT]-[BARCODE]-TC AGT TTG GAG AAG CAA AAA AGA ACA GCT C SEQ ID NO: 102. [5′-Phos]-[SPLINT]-[BARCODE]-GA TCA TCA CAG AAG ACA GAA AGT CCA GCA C SEQ ID NO: 103. [5′-Phos]-[SPLINT]-[BARCODE]-GC AAT CGC TGA AGA CAG AAA GTC CAG TAC SEQ ID NO: 104. [5′-Phos]-[SPLINT]-[BARCODE]-CA GTT TGG TGA TGC AAG AAA GGA CAG TTC SEQ ID NO: 105. [5′-Phos]-[SPLINT]-[BARCODE]-CA GTC AAA GCT GAG GAA CTT TAT GGC CA SEQ ID NO: 106. [5′-Phos]-[SPLINT]-[BARCODE]-CT TCT TAA ACA AAA GTG CCA AGC ACC TCT C SEQ ID NO: 107. [5′-Phos]-[SPLINT]-[BARCODE]-CT GCT TCA TTT AAT GAA AAA AAG CAG CAA AGC TC SEQ ID NO: 108. [5′-Phos]-[SPLINT]-[BARCODE]-TT CTG TGA GCT TCC AGA AAA CAA CTA AAA CTA TTC A SEQ ID NO: 109. [5′-Phos]-[SPLINT]-[BARCODE]-CA CTG TAC TGT TGA ATA AAA ATG CTA AAC ATG TCT C SEQ ID NO: 110. [5′-Phos]-[SPLINT]-[BARCODE]-GC CTG TGA ACT TTG AAA AAA AGA AAA AGT TCA TCA A SEQ ID NO: 111. [5′-Phos]-[SPLINT]-[BARCODE]-CC AAG TTG GAT GAG AAA AAG CAG CAA AGT TC SEQ ID NO: 112. [5′-Phos]-[SPLINT]-[BARCODE]-TC AGT TTG GTA TAA CCA GAA AGG ACA GCT T SEQ ID NO: 113. [5′-Phos]-[SPLINT]-[BARCODE]-AA GTA GCA TAT TAG ATA AGA AAG AAC TTT CCA GCA SEQ ID NO: 114. [5′-Phos]-[SPLINT]-[BARCODE]-CA GGC TTA AAA AAG GAG ACC AGC ACA TTT C SEQ ID NO: 115. [5′-Phos]-[SPLINT]-[BARCODE]-CT TCC AGA AAG CAG CCA AAT CCT TCA G SEQ ID NO: 116. [5′-Phos]-[SPLINT]-[BARCODE]-TG ATA CCA AAG CCC GTC TCA GCA C SEQ ID NO: 117. [5′-Phos]-[SPLINT]-[BARCODE]-GA GGC GGA AAT ATT AAA GAC AAA AAC TCC CC SEQ ID NO: 118. [5′-Phos]-[SPLINT]-[BARCODE]-CC ACA ATA AAC ATA CAG GAA AAG CAC AGC TC SEQ ID NO: 119. [5′-Phos]-[SPLINT]-[BARCODE]-AG AAA GCA GCG AAA TCC GTC GC SEQ ID NO: 120. [5′-Phos]-[SPLINT]-[BARCODE]-TG ACA TTG ATA TTG CAA AGA ACC TGG CTG T SEQ ID NO: 121. [5′-Phos]-[SPLINT]-[BARCODE]-GA AAC ACA TTC TGA CCC AGA AAG CCT TTC A

In one embodiment, a composition containing a plurality of second primers is provided. In some cases, the plurality of second primers are immune cell receptor gene-specific primers. The plurality of immune cell receptor gene-specific primers can be configured to hybridize to, and thus enrich in a polymerase-mediated extension step, a plurality of target polynucleotides in a sample that encode immune cell receptor genes. The second primers can include a universal primer binding site, or complement thereof, and an immune cell receptor hybridizing region. In some cases, the second primers include from 5′ to 3′ a universal primer binding site and an immune cell receptor hybridizing region. In some cases, the second primer immune cell receptor hybridizing region is complementary to, and hybridizes under hybridization conditions with, a J-gene region of an immune cell receptor encoding polynucleotide, or a complement thereof. In some cases, the second primer immune cell receptor hybridizing region is complementary to, and hybridizes under hybridization conditions with, a V region of an immune cell receptor encoding polynucleotide (e.g., a framework 1, framework 2, or framework 3 region), or a complement thereof. In some cases, the second primer immune cell receptor hybridizing region is complementary to, and hybridizes under hybridization conditions with, a C gene region of an immune cell receptor encoding polynucleotide, or a complement thereof.

As described herein, target polynucleotides encoding a TCR β-chain or 6-chain can contain a D region that is positioned between a V region and a J region, whereas target polynucleotides encoding a TCR α-chain or γ-chain can lack a D region, such that the V region and J region are adjacent. Similarly, target polynucleotides encoding a BCR heavy chain can contain a D region that is positioned between a V region and a J region, whereas target polynucleotides encoding a BCR light chain can lack a D region, such that the V region and J region are adjacent.

Second primer extension products of second primers containing a [J] or an [FW] region that are templated by a first primer extension product templated by a TCR β-chain or 6-chain or BCR heavy chain can, e.g., contain a VDJ region, or a portion of the V region, a D region, and a portion of a J region. Similarly, second primer extension products of second primers containing a [J] or an [FW] region that are templated by first primer extension product templated by a TCR α-chain or γ-chain or a BCR light chain can lack a D region, and thus contain a V region or portion thereof adjacent to a J region or portion thereof.

In some embodiments, the plurality of second primers contains at least 2, at least 5, at least 10, at least 25, at least 50, at least 75, or all of the primers set forth in Table 2 (SEQ ID Nos: 122-204. In one embodiment, the plurality of second primers contains at least 1 of the primers set forth in SEQ ID Nos: 122-204. In some embodiments, the plurality of second primers contains at least 2, at least 5, at least 10, or all of the primers set forth in SEQ ID NOS: 205-213. In one embodiment, the plurality of second primers contains at least 1 of the primers set forth in SEQ ID NOS: 205-213.

In one embodiment, the second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene. In another embodiment, the second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene. In another embodiment, the second primers are complementary across their full-length to a framework 1, framework 2, or framework 3 region of an immune cell receptor V gene.

In yet another embodiment, the second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary) to an immune cell receptor J gene region. In another embodiment, the second primers are complementary or substantially complementary (i.e., at least 70%, 75%, 80%, 85%, 90%, 95% or 99% complementary across at least 5, at least 10, at least 15, at least 20 or more nucleotides) to an immune cell receptor J gene region. In another embodiment, the second primers are complementary across their full-length to an immune cell receptor J gene region.

TABLE 2 SEQ ID NO: Sequence SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 122. GGA GAA GTG GAA ACT CTG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGA NO: 123. CTC ACC AGA TAT AAT GAA TAC ATG GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 124. GGA TGC TGA GTC TGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTG NO: 125. TAC AGC CAG CCT GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 126. TGG TTG CAC TTG GAG TCT TGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 127. CGG ATG AAC AAT AAG GCT GGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTT NO: 128. GGT ATG ACC ACC ACT TGG TTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 129. TGA CCA GAA GTC GGG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAT NO: 130. GGA ACT TAC TTG CTT TAA CAA ATA GTC TTG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 131. TGA GTT CCA CTT TTA GCT GAG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 132. CTG GAG AGA CTA GAA GCA TAG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 133. TGA CCA GCA GTC TGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 134. TGG GAT GAC TTG GAG CTT TGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 135. TAC TTA CCA GGT TTT ACT GAT AAT CTT GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 136. CTG GAA CTC ACT GAT AAG GTG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 137. GGA ACT CAC TGA TAA GGT GGG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 138. CTT ACT AAG ATC CAC CTT TAA CAT GGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 139. TTG GTT TAA CTA GCA CCC TGG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAG NO: 140. GCC AGA CAG TCA ACT GAG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 141. CAC TTA CTT GGA GTG ACA TTA TGT TTG GAT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 142. CTT ACT TGC TCT TAC AGT TAC TGT GGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 143. ACT TAC TTG GTT TTA CAT TGA GTT TGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 144. CCA GGT AAA ACA GTC AAT TGT GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 145. TGG GTT TCA CAG ATA ACT CCG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 146. TGA CCA CAA CCT GGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGC NO: 147. TTG ACA AGC AGC CTT GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGC NO: 148. AGC ACG GAC AAT CTG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 149. CTT CAC AGT GAG CGT AGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 150. TGG TAT GAC CGA GAG TTT GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 151. TTG CAA TCA CAG AAA GTC TTG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 152. GGG GAG AAT ATG AAG TCG TGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGC NO: 153. TTC ACC ACC AGC TGA GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 154. GGA CAG CAA GCA GAG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGA NO: 155. CTT ACC TGG CTT TAT AAT TAG CTT GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 156. CTT ACT TGG AAA GAC TTG TAA TCT GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 157. TAC GTG GTA AAA CAA TCA CTT GAG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 158. GGA ATA ACG GTG AGT CTC GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 159. TAC CTG GTT TTA CTT GGT AAA GTT GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCG NO: 160. GAT TTA CTG CCA GGC TTG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCG NO: 161. GGG TTT GAC CAT TAA CCT TGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGC NO: 162. TAA AAC CTT CAG CCT GGT GCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGT NO: 163. GAC CAA CAG CGA GGT GCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 164. ACT TAC TTG GTT TAA CAG AGA GTT TAG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 165. TTG GTT TTA CTG TCA GTC TGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCG NO: 166. AGC GTG ACC TGA AGT CTT GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 167. GGG CTG GAT GAT TAG ATG AGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 168. GCC TAA CTG CTA AAC GAG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 169. CAG GAC TTG ACT CTC AGA ATG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 170. TGG GTA TGA TGG TGA GTC TTG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 171. TGG AAT GAC CGT CAA ACT TGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 172. TTA CTT GGA ATG ACT GAT AAG CTT GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTG NO: 173. CTT GGC TTC ACA GTT AGT CAT GTC TC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 174. TGG ATG GAC AGT CAA GAT GGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAA NO: 175. CTT ACT TGG ATT CAC GGT TAA GAG AGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTT NO: 176. GGG TTG ATA GTC AGC CTG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 177. ACA CTT ACT TGG ATT TAT TTT TGT ACT CAT CCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 178. AAA CAT ACC TGG TCT AAC ACT CAG AGT TAT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 179. CAT GGG TTT ACT GTC AGT TTC GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 180. AGG ATT CAC TGT GAG CTG TGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAG NO: 181. CTT CAC TCT CAC TTG CGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 182. CAG GCT CAC AAT TAA CTC AGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTA NO: 183. CTT GCT GAG TTT CAT GAT TCC TCT AGT GTT SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGT NO: 184. TCC ACA GTC ACA CGG GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 185. GGT TCC ACG ATG AGT TGT GTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGG NO: 186. CTC CAC GAA GAG TTT GAT GCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 187. TAC GTT GTT GTA CCT CCA GAT AGG TTC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGT NO: 188. CTT ACC TAC AAC TGT GAG TCT GGT GCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 189. TTA CCT ACA ACG GTT AAC CTG GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 190. TAC TCA CCT ACA ACA GTG AGC CAA CTT CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAT NO: 191. ACC CAA GAC AGA GAG CTG GGT TCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAA NO: 192. CTT ACC TAG GAT GGA GAG TCG AGT CCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 193. GTC ACA GTG AGC CTG GTC CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 194. CGG TGA GCC GTG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCC NO: 195. AGT ACG GTC AGC CTA GAG CC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 196. CTG TCA GCC GGG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 197. CTG AGA GCC GGG TCC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TAC NO: 198. CAG GAG CCG CGT GCC SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCA NO: 199. CGG TCA GCC TGC TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGA NO: 200. CCG TGA GCC TGG TGC C SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TGT NO: 201. GAA GTT ACT ATG AGC TTA GTC CCT TCA GCA AA SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCG NO: 202. AAG TTA CTA TGA GCC TAG TCC CTT TTG CAA A SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TTG NO: 203. ACA ACA AGT GTT GTT CCA CTG CCA AA SEQ ID AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC TCT NO: 204. GTA ATG ATA AGC TTT GTT CCG GGA CCA AA

In some embodiments, the composition is a first primer extension primer mixture comprising V-gene specific primers for one or more immune sequence genes. In some embodiments, a first primer extension primer mixture includes primers for one or more of TCR-alpha, TCR-beta, TCR-gamma, TCR-delta and immunoglobulin (IGH, immunoglobulin heavy chain, IGL, immunoglobulin light chain-lambda and IGK, immunoglobulin light chain-kappa). In some embodiments, the mixture comprises multiple primers, e.g., 69 TCR-beta, 8 TCR-deta and 138 IGH V-gene primers.

In some embodiments, the composition is a second primer extension primer mixture comprising J-gene specific primers for one or more immune sequence genes. In some embodiments, a second primer extension primer mixture includes primers for one or more of TCR-alpha, TCR-beta, TCR-gamma, TCR-delta and immunoglobulin (IGH, immunoglobulin heavy chain, IGL, immunoglobulin light chain-lambda and IGK, immunoglobulin light chain-kappa). In some embodiments, the mixture comprises multiple primers, e.g., 14 TCR-beta, 4 TCR-deta and 9 IGH J-gene primers.

In some embodiments, the V-gene primers and J-gene primers for various genes were selected from Table 2a.

TABLE 2a V-gene and J-gene primers primers SEQ  ID NO: NAME SEQUENCE 338 IGHV3-38 GGTAGCACATACTACGCAGACTCC 339 IGHV3-22 GGACAACAGAATAGACCACGTCTGT 340 IGHV3OR16-8 ACAACGCCAATAACTCACCGTATCT 341 IGHVII-30-21 GGAGCACAAATTACAACCCACTTCTC 342 TRBV7-3 GGGCTGCCCAAAGATCGGT 343 IGHV3-30 CAGAGACAATTCCAAGAACACGCTG 344 IGHV7-34-1 TGTCAGCACGGCGTGTCTT 345 TRBV5-3 AGGGCGCCAGTTCCATGAC 346 TRBV15 ACACCCCTGATAACTTCCAATCCAG 347 IGHV1-58 CAGTGGTAACACAAACTACGCACAG 348 TRBV12-1 CCTGATGTATCATTCTCCACTCTGAGG 349 IGHV3OR16-6 GATTCACTTGCAGTAACGCCTGG 350 IGHV1OR16-1 GAGGGATCTACTCTGGCAATGGTAAG 351 TRBV12-3 CAACAACGTTCCGATAGATGATTCAGG 352 TRBV30 TACTCCGTTGGTATTGGCCAGATC 353 TRBV7-4 CAGAGTGATGCTCAACGAGACAAATC 354 IGHV7-56 TCTGTCAGCACGGCGGATC 355 TRBV5-6 TCACCAGTTCCCTAACTATAGCTCTGA 356 TRBV11-2 CAGTTGCCTAAGGATCGATTTTCTGC 357 TRBV1 CTGACAGCTCTCGCTTATACCTTCAT 358 TRBV28 CTCTAGAGAGAAGAAGGAGCGCTTC 359 TRBV27 TGAAGGGTACAAAGTCTCTCGAAAAGA 360 IGHVIII-82 GCAACAGTGAGTTATCAGGGTTACTCT 361 IGHVII-28-1 AATTGTATCTGCTTGCCCCTAGAAGAT 362 IGHV1OR15-3 CGCTGGCAATGGTAACACAAAATATTC 363 IGHV1-24 GTGAAACAATCTACGCACAGAAGTTCC 364 IGHV7-4-1 CACCTCTGTCAGCACGGCA 365 IGHV3-35 GTAGGACGCACTATGCAGACTCTG 366 TRBV6-5 CCACAGAGGATTTCCCGCTCA 367 IGHV3-60 GTGGTGATACCGTACTCTACACAGAC 368 IGHV4-4 CCCTCAAGAGTCGAGTCACCATATC 369 IGHVIII-5-2 GGGGACAACACTTAACATCACAATCTC 370 IGHV1OR16-4 GTGTCCTCCCCACAGGTGC 371 TRBV10-1 TTCACGACACTAACAAAGGAGAAGTCT 372 IGHV1OR16-2 GTAAGACAGGCTATGCACAGAAGTTTC 373 IGHV3-43 GTAGCACATACTATGCAGACTCTGTGA 374 TRBV5-1 TCGATTCTCAGGGCGCCAG 375 TRBV4-1 CCAAGTCGCTTCTCACCTGAATG 376 IGHV3-47 CCATCTCCAGAGACAACGCCA 377 TRBV3-1 AGTTCCAAATCGCTTCTCACCTAAATC 378 IGHV1-2 TGGCACAAACTATGCACAGAAGTTTC 379 IGHV3-54 ATGTTATGCACAATCTGTGAAGAGCAG 380 TRBV16 CAAGGAAAGATTTTCAGCTAAGTGCCT 381 TRBV9 AACATTCTTGAACGATTCTCCGCAC 382 IGHV1-67 CCTGCAAGACTTGTGGATACACCTA 383 IGHV7-27 AGTCAAGTGAGACTTCACGCACT 384 IGHV3-79 CGAGCAGATTCACCGTCTCCA 385 IGHV3-63 AGGACGTTTGTGTATTTTCAGGTGTTC 386 TRBV24OR9-2 CGGTTGATCTATTGCTCCTTTGATGTC 387 IGHVIII-11-1 TTGTACAGCCCAGCGGTTCA 388 TRBV7-1 AGCAGACAAATCGGGGCTTCC 389 IGHVII-53-1 CTCCAGATCCATGTCCAAAAAGCAG 390 TRBVB CTGAGTCAGCATAGTCATTCCAACCA 391 IGHV3OR16-10 AGAGACAATGCCAAGAACTCCTTGTAT 392 TRBV13 GATAAAGGAAGCATCCCTGATCGATTC 393 IGHV1-17 AATGATAACACACACTACGCACAGAAG 394 TRBV6-1 CAATGTCTCCAGATTAAACAAACGGGA 395 TRBV10-2 AGTCCCCGATGGCTACGTTG 396 TRBV23-1 CACAAGAAGCGATTCTCATCTCAATGC 397 IGHV2OR16-5 AATGACAAAAAATCCTACAGCACGTCT 398 IGHV3OR16-12 GTAGTAGTGGTTGTAGCACAAACTACG 399 IGHV1-45 GTAACACCAACTACGCACAGAAATTCC 400 IGHV3-49 TACGCCGCGTCTGTGAAAGG 401 IGHVII-43-1 CTCCAGATCTATGTCCAAAAACAGCTC 402 IGHV3-76 GGTACAGCTTGGGGGGTCC 403 IGHVII-51-2 GCATAGGTCACGAGGGAGCA 404 IGHV5-51 AGTCCATCAGCACCGCCTAC 405 IGHVIII-26-1 TGGTTTCGGGTTTACTGGGTGC 406 TRBV6-7 AATGTCTCCAGATCAAACACAGAGGAT 407 TRBV7-6 GGCTGCCCAATGATCGGTTC 408 IGHV3-42 CTCATTTGCAGCTTCTAGATTCACCTT 409 TRBV25OR9-2 CTCCAGAATAAGGATAGAGCGTTTTCC 410 TRBV8-2 GAACAGTGTTCTGATATCGACAAGACC 411 TRBV5-2 GGAAACTTGCCTAATTGATTCTCAGCT 412 IGHVII-44-2 TCCTTCTCCAGAGATTCATCCAAGAAA 413 TRBV25-1 GTCTCCAGAATAAGGACGGAGCATTT 414 IGHV8-51-1 ATATGGCGTGGTGAAAGTCATCAATAC 415 TRBV7-2 GGCTGCCCAGTGATCGCTT 416 TRBV22-1 GAGATCTAACTGAAGGCTACGTGTCT 417 IGHV1OR15-6 TTGAGTGGATGGAACGTGTTGATCC 418 IGHV1-68 TGGTAACACCAACTATGCAAAGAAGTT 419 IGHVII-62-1 CATAGGTCATGAAGGGAGCACACATTA 420 IGHV3OR16-16 GTGACAGAACAGTGGCTATGTGTG 421 IGHV3-50 CCTGAGACTCTGCCGTGCA 422 IGHV7-81 CAGGGCTTCACAGGACGGT 423 IGHV3-41 CTCCAGAGACAATTCTAAGAGCATGCT 424 IGHV3-29 GCCGAGTTCACCAGTCTCCA 425 TRBV20-1 CCACATACGAGCAAGGCGTC 426 TRBV18 GCCAAAGGAACGATTTTCTGCTGAAT 427 IGHV3-25 GCAAAGCCTGCGTGGTCC 428 IGHV3-15 CGCTGCACCCGTGAAAGG 429 TRBV17 CAGTACCAAAACATTGCAGTTGATTCA 430 IGHVII-74-1 ACTACATCACAAACAGTGCTTATGACT 431 TRBV19 AGAAAGGAGATATAGCTGAAGGGTACA 432 IGHV7-40 ACCAACGGCTTCACAGGACG 433 IGHVII-22-1 TGCTTCTCCATTACAACCAGTGCTT 434 TRBV24-1 AAAGGAGAGATCTCTGATGGATACAGT 435 IGHV3-16 CTCCGTGAAGCGCCGATTC 436 TRBV5-4 TCTCCAGTTCCCTAATTATAGCTCTGA 437 IGHVII-33-1 CATCTCCAGATCCATGTCCAAAAAGTA 438 IGHV4-80 GGTGCAGCTGCAGGAGTGG 439 IGHV1OR15-4 GGTAACACAACATATGCACAGAAGTTC 440 TRBV14 CAACAATCGATTCTTAGCTGAAAGGAC 441 TRBV5-5 AGCTCGCCAGTTCCCTAACTATAG 442 IGHV3OR16-11 CACATACTATGCAGACTCCGTGAAG 443 IGHV3OR15-7 AGCTAACAGTTACACGACAGAATATGC 444 IGHVIII-13-1 GTCAGACAGAGAAATACTACAGACCAG 445 IGHVIII-38-1 ACTCGCCTTCAGTACAAAGAAGATTAA 446 IGHV3-57 AAGTGGGAGTTCTCAGAGTTACTCTCC 447 IGHV1-69-2 GTCACCATAACCGCGGACAC 448 IGHV1-14 AGGGACACGTCCACGAGC 449 TRBV29-1 CCAAACCTAACATTCTCAACTCTGACT 450 IGHVII-65-1 CATCCATCACCCCCCGCA 451 IGHV3-32 GATGATGGAAGTCAGATACACCATGCA 452 IGHV3-6 GGGTCCCAGTTATTAGTGGTAGTGGTA 453 IGHV3-52 AAAGTGTGACGGAAGTGAGAAATACTA 454 IGHVIII-2-1 GAGTGATCAAGTATGAATTCTCAGGGT 455 TRBV12-2 CCTGATGGATCATTCTCTACTCTGAAG 456 IGHV3-37 GAATGGGTCTCATACATTAGTGCTAGT 457 TRBV20OR9-2 GGCTCCGAGGTCACATACGA 458 IGHV4-55 TCGAATCACCATGTCCGTAGACA 459 IGHVII-49-1 TGCTTCTCCATCACAACCAGTG 460 TRBV6-8 GCTGCTGGTACTACTGACAAAGAAGTC 461 TRBV7-5 CCTTCCAGGATGAAACTCAACAAGATA 462 IGHV1-69D CACGATTACCGCGGACGAAT 463 TRBV26OR9-2 GAGATGTCTCTGAGAGGTATCATGTTT 464 IGHV3OR16-7 CTGGAGTGGGTTGGCCGTAT 465 IGHV2-5 ATTTATTGGGATGATGATAAGCGCTAC 466 TRBV21-1 AGAAAGCAGAAATAATCAATGAGCGAT 467 TRBV2 GCCTGATGGATCAAATTTCACTCTGA 468 IGHV3-30-2 ACAGTGTGATGGAAGTCAGATATGTTA 469 TRBV22OR9-2 CTGAGACTGATCTATTACTCAAGGGTT 470 TRBV26 CCCTGTCTCTATTTGATCATCCATTTT 471 TRBVA GCCGACTCATTATTCAGTTAACATTGA 472 TRBV6-2 GATGGCTACAATGTCTCCAGATTAAAA 473 TRBV6-4 CCATTATTCAAATACTGCAGGTACCAC 474 TRBV7-7 CAATTATGAAGCTCAACCAGACAAATC 475 TRBV7-9 CTTACTTCCAGAATGAAGCTCAACTAG 476 TRBV10-3 TGGTGTTAAAGATACTGACAAAGGAGA 477 IGHV1OR15-2 ACACTTACAATGGTAACACAAACTACC 478 IGHV3-36 TCATTTATGAGTTGTTGTGTAGGTAGC 479 IGHV3-75 GTCTCATGTATTAGTACTGATGGGAGT 480 IGHVII-1-1 GCCCTCTGGGAAGGCGCT 481 IGHVII-15-1 GGATTTCCAATCATAACCAGTACTTCC 482 IGHVIII-44 ACACTTTACAGACACCATCAATTTTCC 483 IGHVIII-76-1 ACCCTCCATCAATACAAAGAAAAATCA 484 IGHVIV-44-1 GTGATATGGGTTAAGGGAAACACTAAG 485 IGHV1-18 CGCTTACAATGGTAACACAAACTATGC 486 IGHV2-70 TGGGATGATGATAAATACTACAGCACA 487 IGHV2-70D TTGGGATGATGATAAATTCTACAGCAC 488 IGHV4-28 CTATTATAGTGGGAGCACCTACTACAA 489 IGHV6-1 GTCCAAGTGGTATAATGATTATGCAGT 490 IGHVII-26-2 TAGACTGGATCATCAAGGAATACACAT 491 IGHV3OR16-13 GCACAAGCTACGCAGACTCC 492 IGHV3-13 GGTGACCCATACTATCCAGGCT 493 TRBV8-1 AGCATGACCAAAGGCGGTG 494 TRBV12-5 GCAACCGGGCTCCTCTAGA 495 IGHV3-73 ATGCTGCGTCGGTGAAAGG 496 IGHV5-78 CCTTCCAAGGCCACGTCA 497 IGHV1OR15-9 AACCAGGGACACATCCATGG 498 IGHV1OR21-1 TAGTGATGGCAGCACAAGCT 499 IGHV1-69 CACGATTACCGCGGACAAATC 500 IGHV3OR16-9 GTGGTTACACAAACTACGCAGAC 501 IGHV3OR16-15 CGGTAAGACGCACTATGTGGA 502 IGHV2-26 TCGAATGACGAAAAATCCTACAGC 503 IGHJ3 GTCACCGTCTCTTCAGGTAAGATGG 504 TRBJ1-6 CTCTTGACTCGGGGGTGCC 505 TRBJ2-4 GCTCGGGTTTTTGTGCGGG 506 TRBJ1-3 TGTTGTAGGTGAGTAAGTCAAGGCTG 507 IGHJ2 GAGTCCCACTGCAGCCCC 508 IGHJ6 CCTCAGGTAAGAATGGCCACTCTAG 509 TRBJ2-3 CGTCGCAGGGCCAGTTTCT 510 TRBJ2-7 AGTCGGAGGGTGGACCGG 511 TRBJ1-5 CTCTCCATCCTAGGTAAGTTGCAGAAT 512 IGHJ1 GGTCACCGTCTCCTCAGGTG 513 TRBJ2-6 GTGAGTTTTCGCGGGACCAC 514 IGHJ3P TACGTGGGAGGCCAGCAGA 515 TRBJ1-2 GTTAACCGTTGTAGGTAAGGCTGG 516 TRBJ2-1 CACGACCCCAGAACCCTGT 517 TRBJ1-4 GATAGTGTATCATAAGGTCGGAGTTCC 518 TRBJ2-2 TGGGTAAGGAGGCGGTTGG 519 TRBJ2-5 TTGGGTCTGGTTTTTGCGGG 520 TRBJ1-1 TGTCCCTTTTAGAGTGGCTATATTCTT 521 IGHJ2P GGTCTCAGCCCGGGGGTC 522 IGHJ1P CCTACCAGCCGCAGGGTT 523 TRBJ2-2P GCACCGGTTTTTGTCCTGG

In some embodiments, the composition is a second primer extension mixture comprising J-gene specific primers and further comprising an opposite-facing primer capable of hybridizing to a primer binding site (universal primer binding site) in the first primer extension primer. In some embodiments, the opposite-facing primer is a shortened sequencing primer. In some embodiments, opposite-facing primer is a sequencing primer to be used in a subsequencing sequencing step, the primer being shortened by removing the index sequence.

Described herein are target polynucleotides and compositions containing such target polynucleotides. In some cases, a composition containing such target polynucleotides further contains a DNA-dependent polymerase and/or a RNA-dependent DNA polymerase, a ligase, a first primer or plurality of first primers, a second primer or plurality of second primers, first or second primer polymerase extension products, or a combination thereof. Generally, the target polynucleotides encode immune cell receptors, such as B cell receptors (i.e., antibodies), or T cell receptors, a complement thereof, or portions thereof. The target polynucleotides can be single stranded or double-stranded. The target polynucleotides can be DNA (e.g., genomic DNA). The target polynucleotides can be RNA (e.g., mRNA). The target polynucleotides can be cDNA generated by reverse transcription of mRNA. In an exemplary embodiment, the target polynucleotides are genomic DNA or cDNA that is heat denatured to form single-stranded targets.

In some embodiments, the target polynucleotides are obtained from a sample enriched for immune cells. For example, the target polynucleotides can be obtained from a sample enriched for T cells, enriched for B cells, enriched for T cells and B cells, enriched for lymphocytes, or enriched for peripheral blood mononuclear cells (PBMCs). In some cases, the target polynucleotides are obtained from a sample enriched for a fraction of T cells or B cells. For example, the sample can be enriched for T cells that express α/β TCRs. As another example, the sample can be enriched for T cells that express γ/δ TCRs. As yet another example, the sample can be enriched for B cells that express a certain isotype of BCR, or a set of such isotypes, such as IgA, IgG, IgM, IgE, or a combination thereof. As yet another example, the sample can be enriched for B cells expressing kappa light chain BCRs. As yet another example, the sample can be enriched for B cells expressing lambda light chain BCRs. As yet another example, the sample can be enriched for T cells that express α/β TCRs or γ/δ TCRs, wherein the sample is obtained by flow cytometry. As yet another example, the sample can be a FFPE tissue sample containing infiltrating lymphocytes. As yet another example, the sample can be a FFPE tissue sample, wherein the sample contains, or is suspected of containing, one or more tumor cells. Methods for enriching sample for a specific immune cell type include, but are not limited to, methods employing one or more of the following: ultracentrifugation, FICOLL™ gradient centrifugation, or flow cytometry (e.g., fluorescence-activated cell sorting (FACS)).

Described herein are reaction mixtures that contain target polynucleotides (e.g., target polynucleotides encoding B or T cell receptors, a complement thereof, or portions thereof), first primers, first primer extension products (e.g., single-stranded or hybridized to a target polynucleotide), second primers, second primer extension products (e.g., single-stranded or hybridized to a target polynucleotide), adapters (e.g., double stranded adapters, such as splint adapters), or a combination thereof. In some cases, the reaction mixture further contains a DNA-dependent DNA polymerase and/or a RNA-dependent DNA polymerase and reagents for polymerase-mediated and template-directed primer extension (e.g., divalent cations such as magnesium cations, nucleotide triphosphates, buffers, salts, etc.). In some cases, the DNA polymerase exhibits strand-displacing activity. In some cases, the DNA polymerase exhibits exonuclease activity. In some cases, the DNA polymerase does not exhibit or does not exhibit substantial strand-displacing activity. In some cases, the DNA polymerase does not exhibit or does not exhibit substantial exonuclease activity. In some cases, the DNA polymerase is thermostable. In some cases, the reaction mixture contains DNA ligase. In some embodiments, the RNA-dependent DNA polymerase is a telomerase. In some embodiments the RNA-dependent DNA polymerase lacks 3′-5′ exonuclease activity. In some embodiments, the RNA-dependent DNA polymerase is thermostable.

In some embodiments, the DNA polymerase has long-range capability. In some embodiments, the DNA polymerase has proofreading capability including processing proofreading capability. In some embodiments, the DNA polymerase has high fidelity. In some embodiments, the DNA polymerase is a mixture including Taq polymerase and an engineered archaeal B-family polymerase. In some embodiments, the polymerase has hot-start capability. In some embodiments, the hot-start capability is conferred by a thermolabile polymerase-specific antibody.

In some embodiments, the reaction mixture comprises an exonuclease. In some embodiments, the exonuclease is a single-strand exonuclease. In some embodiments, the exonuclease is thermolabile. In some embodiments, the exonuclease is inactivated at or below 95° C. In some embodiments, the exonuclease is inactivated at 80° C.

In some embodiments, the reaction mixture contains a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality each comprise immune cell receptor V gene regions, optionally D gene regions, optionally C gene regions, and J gene regions (e.g., target polynucleotides encoding immune cell receptor VJ, VDJ, or VJ and VDJ regions); and a plurality of first primers having [FW]regions. In some embodiments, the reaction mixture contains a plurality of structurally different target polynucleotides, wherein individual target polynucleotides of the plurality each comprise immune cell receptor V gene regions, optionally D gene regions, optionally C gene regions, and J gene regions (e.g., immune cell receptor VJ, VDJ, or VJ and VDJ regions); and a plurality of first primers having [J] regions or [C] regions.

In some embodiments, the first primers of the reaction mixture are hybridized to the target polynucleotides of the reaction mixture. In some embodiments, the reaction mixture contains a plurality of structurally different target polynucleotides hybridized to a plurality of first primer extension products (i.e., products of a DNA-polymerase-mediated and template-directed extension reaction). In some embodiments, the reaction mixture contains a plurality of structurally different immune cell receptor encoding target polynucleotides hybridized to a plurality of first primer DNA polymerase extension products.

In some embodiments, the reaction mixture contains a plurality of single-stranded target polynucleotides, the individual target polynucleotides each comprising the following from regions from 5′ to 3′: a sequencer-specific adapter sequence, optionally a multiplex identifier (MID) barcode, a unique molecular identifier (UID) barcode, at least a portion of an immune cell receptor framework 3 region, an immune cell receptor CDR3 region, an optional immune cell receptor diversity (D) region, an optional immune cell receptor constant (C) region, and at least a portion of an immune cell receptor J region, or the complements thereof. In some cases, such a plurality of single-stranded target polynucleotides are first primer extension products. In some cases, such a plurality of single-stranded target polynucleotides are first primer extension products ligated to an adapter comprising a universal primer binding site and optionally an MID barcode.

In some embodiments, the reaction mixture contains a plurality of single-stranded target polynucleotides, the individual target polynucleotides each comprising the following from regions from 5′ to 3′: a sequencer-specific adapter sequence, optionally a multiplex identifier (MID) barcode, a unique molecular identifier (UID) barcode, at least a portion of an immune cell receptor J-gene region, an optional D region, an optional immune cell receptor constant (C) region, an immune cell receptor CDR3 region, and at least a portion of an immune cell receptor framework 3 region, or the complements thereof. In some cases, such a plurality of single-stranded target polynucleotides are first primer extension products. In some cases, such a plurality of single-stranded target polynucleotides are first primer extension products ligated to an adapter comprising a universal primer binding site and optionally an MID barcode.

In some embodiments, a reaction mixture can contain one or more of the foregoing first primer extension products (e.g., adapter ligated first primer extension products) hybridized to a plurality of second primer extension products. In cases where the first primers hybridize to a framework region of an immune cell receptor encoding target polynucleotide, the second primers can be configured to hybridize to a J gene region or C gene region of the first primer extension products. In cases, where first primers hybridize to a complement of a J region or C region of an immune cell receptor encoding target polynucleotide, the second primers can be configured to hybridize to a framework region of the first primer extension products.

Described herein are adapters for downstream amplification or sequencing applications. Attachment of an adapter to one or both ends of a target polynucleotide, first primer extension product, or second primer extension product, can attach a UID barcode, an MID barcode, a universal primer binding site or complement thereof, or a combination thereof. Adapters containing a universal primer binding site or complement thereof can be referred to as universal adapters. In some embodiments, adapters are attached by ligation. In some embodiments, adapters are attached by hybridizing a primer containing an adapter sequence (e.g., an adapter sequence comprising or consisting of a universal primer binding site or complement thereof) to a target polynucleotide, first primer extension product, or second primer extension product. In some embodiments, the primer containing an adapter sequence is a second primer that can be hybridized to a first primer extension product and extended with a polymerase as described herein. In some embodiments, first adapters are ligated to a first primer extension product and second adapters are attached by hybridization of a second primer containing such an adapter to the first primer extension product and extending the second primer.

In some embodiments, one or more adapters are splint adapters. Splint adapters can be hybridized to a [SPLINT] region of a primer extension product (e.g., a first primer extension product) and ligated to a [5′-Phos] of the first primer extension product. Splint adapters can contain a double stranded region and a 5′ single-stranded overhang region, wherein the 5′ single-stranded overhang region is complementary to and hybridizes under hybridization conditions with the [SPLINT] region of the primer extension product (e.g., a first primer extension product). The 5′ single-stranded overhang region can be at least 2 nucleotides in length, at least 4 nucleotides in length, at least 6 nucleotides in length, at least 8 nucleotides in length, from 2 to 10 nucleotides in length, or from 2 to 8 nucleotides in length. In some embodiments, the 5′ single-stranded overhang region comprises or consists of 6 consecutive nucleotides that are complementary to the [SPLINT] region of the first primer extension product. In some embodiments, the 5′ single-stranded overhang region comprises or consists of the sequence AGA TCG.

Splint adapters can contain a barcode and a universal primer binding site as described herein. In some cases, the splint adapter contains a MID barcode. In some cases, the splint adapter contains an MID barcode and a universal primer binding site. In some cases, the barcode is encoded in the double-stranded region of the splint adapter. In some cases, the universal primer binding site is encoded in the double-stranded region of the splint adapter. In some cases, the barcode (e.g., MID barcode) and the universal primer binding site is encoded in the double-stranded region of the splint adapter. In some embodiments, with respect to the strand of the splint adapter that contains the 5′ single-stranded overhang region, in some cases, the universal primer binding site can be 3′ of the barcode (e.g., MID barcode).

In some embodiments, the reaction mixture contains universal amplification primers hybridizing to adapter sequences or universal primer binding sites in first and second round primer extension primers. The universal amplification primers may comprise sequencing platform-specific sequences. Based on the platform, the sequencing primers may include barcode (index) sequences, e.g., sample index sequences. One or both sequencing primers may comprise index sequences.

In some embodiments, prior to universal amplification with universal primers, excess primers from the second round of primer extension is removed by an exonuclease. In some embodiments, the exonuclease is added to a reaction mixture comprising excess extension primers to be degraded and also comprising universal amplification primers to be retained. In some embodiments, universal amplification primers comprise one or more modifications conferring exonuclease resistance.

In some embodiments, the nuclease-protecting modification allows to advantageously skip a purification step between the second primer extension and universal amplification thus saving time, resources and reducing the possibility of sample contamination.

In some embodiments, the exonuclease is a 3′-5′-exonuclease and the modification is selected from one or more nucleotides at the 3′-end modified with one of the following: a phosphorothioate (PS) bond, a 2′-O-methyl (2′OMe), a 2′-fluoride and Inverted ddT. In some embodiments, the modification is a nucleotide with a phosphorothioate (PS) bond, which substitutes a sulfur atom for a non-bridging oxygen in the phosphate backbone of an oligonucleotide. In some embodiments, the modification is a nucleotide with 2′-O-methyl (2′OMe) modification of the ribose/deoxyribose yielding 5- to 10-fold reduced susceptibility to DNases. In some embodiments, the modification is a nucleotide with 2′-fluoro modification. The fluorine-modified ribose/deoxyribose confers some relative nuclease resistance. In some embodiments, the modification is a 2′,3′ dideoxy-dT base (5′ Inverted ddT) at the 3′ end of an oligonucleotide protecting against some forms of enzymatic degradation. In some embodiments, the universal primer has more than one modified nucleotide and more than one type of modified nucleotide.

II. Methods

Described herein are methods for performing flanking primer (FP-) primer extension target enrichment (PETE) of target polynucleotides from a sample. In some embodiments, the target polynucleotides encode immune cell receptors, or portions thereof. In such embodiments, the methods can be referred to as immuno-PETE. The methods described herein can utilize a plurality of immune cell receptor V gene specific first primers each comprising an [FW] region at a 3′ end for hybridizing to a framework (e.g., framework 1, framework 2, or framework 3) region of a target polynucleotide encoding an immune cell receptor. In such embodiments, the plurality of second primers each comprise a [ ] region to flank the region of interest. Alternatively, the methods can utilize a plurality of immune cell receptor J gene specific first primers each comprising a [J] region at a 3′ end for hybridizing to a J region of a target polynucleotide encoding an immune cell receptor. In such embodiments, the plurality of second primers each comprise a [FW] region to such that the first and second primers flank the region of interest in the target polynucleotides. In another embodiment, the methods can utilize a plurality of immune cell receptor C gene specific first primers each comprising a C-segment region at a 3′ end for hybridizing to a C gene region of a target polynucleotide encoding an immune cell receptor. In such embodiments, the plurality of second primers can each comprise a [V] gene region such that the first and second primers flank the region of interest in the target polynucleotides.

In some embodiments, the method includes: a) providing a reaction mixture containing: i) a plurality of structurally different target polynucleotides as described herein, wherein the individual target polynucleotides encode immune cell receptor V gene regions, optionally D gene regions, optionally C gene regions, and J gene regions; and, ii) a plurality of immune cell receptor V gene specific primers or C gene specific primers (i.e., first primers) as described herein, wherein the immune cell receptor V gene specific primers are hybridized to the V gene regions of the target polynucleotides or wherein the immune cell receptor C gene specific primers are hybridized to the C gene regions of the target polynucleotides; b), extending the hybridized immune cell receptor V gene specific primers or C gene specific primers with a polymerase to generate extended immune cell receptor V gene specific primers or extended immune cell receptor C gene specific primers (i.e., first primer extension products) and then removing un-extended immune cell receptor V or C gene specific primers, if present, thereby generating extended immune cell receptor V gene specific primers containing at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region or at least a portion of the immune cell receptor C region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor V region. In some cases, the removing un-extended immune cell receptor V or C gene specific primers includes contacting the un-extended immune cell receptor V or C gene specific primers with a single-stranded DNA exonuclease enzyme and thereby digesting the un-extended immune cell receptor V or C gene specific primers.

In some embodiments, the invention is a method comprising the following steps: DNA extraction, optional DNA quality assessment, first round of primer extension, thermolabile exonuclease treatment, purification, second round of primer extension and optional purification thereby forming a library of enriched nucleic acid sequences. Depending on the downstream use of the enriched library, the method may further comprise one or more of the following: library amplification, purification, quality control assessment, pooling of libraries and sequencing of the libraries or pools.

In some embodiments, the first primer extension step comprises two or more repetitions of the annealing step. In some embodiments, the annealing step comprises a temperature profile including several (e.g., 2, 3 or more) progressively lower annealing temperatures. The inventors have discovered that utilizing a step-wise annealing procedure increases specificity of the target enrichment method. The inventors have further discovered that utilizing repetitions of the step-wise annealing procedure further increases specificity of the target enrichment method. Disclosed herein is an improved primer extension target enrichment method wherein the annealing temperature profile comprises one or more of a series of decreasing temperatures. In some embodiments, the annealing step comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 20 or more rounds of thermocycling through the series of two or more annealing temperatures. In some embodiments, by way of example, the annealing step comprises 20 cycles wherein each cycle consists of an incubation at 60° C., at 57.5° C. and at 55° C.

In some embodiments, the first primer extension step comprises a round of denaturation, two or more rounds of step-wise annealing, and a round of extension.

In some embodiments, the first primer extension step utilizes the following temperature profile: [initial denaturation]-[two or more rounds of the annealing temperature profile]-[extension]. In some embodiments, by way of example, the first primer extension step utilizes the following temperature profile:

Stage Temp (° C.) Duration Cycles Initial Denaturation 95° C. 10 min 1 Intermediate Temp 80° C. 0 sec Annealing (ramp at 0.2° C./sec) 60° C. 0 sec Annealing high 60° C. 20 sec 20 Annealing mid 57.5° C. 20 sec Annealing low 55° C. 20 sec Extension 72° C. 2 min 1 End 4° C. ∞ 1

In some cases, the removing un-extended immune cell receptor V or C gene specific primers includes solid phase reversible immobilization of single-stranded first primer extension products or double stranded polynucleotides containing single-stranded target polynucleotide hybridized to single-stranded first primer extension product. In some cases, the removing un-extended immune cell receptor V or C gene specific primers includes resin (e.g., silica (e.g., silica bead)) or membrane-based column or batch purification of double-stranded DNA from single-stranded DNA or purification of a selected size of single or double stranded DNA from the reaction mixture. In some cases, the removing includes removing single or double-stranded DNA, or a combination thereof, having a size of less than about 100 bases or base pairs. In some cases, the removing includes removing single or double-stranded DNA, or a combination thereof, having a size of more than about 1,000 bases or base pairs. In some cases, the removing includes purifying from the sample primer extension products or double-stranded DNA containing primer extension products, or a combination thereof, having a size of more than about 100 bases or base pairs and less than about 1,000 bases or base pairs. In some cases, the removing further removes genomic DNA or denatured (e.g., single-stranded) genomic DNA from the sample. In some embodiments, the removing further removes denatured cDNA from the sample.

In some embodiments, the method includes: c) hybridizing a first universal adapter (e.g., a splint adapter containing a universal primer binding site) to a [SPLINT] adapter hybridization site of the extended immune cell receptor V or C gene specific primers; d) ligating the hybridized first universal adapter to the extended immune cell receptor V or C gene specific primers, and then removing un-ligated adapters, if present. In some cases, the removing un-ligated adapters includes solid phase reversible immobilization of adapter-ligated single-stranded first primer extension products or double stranded polynucleotides containing single-stranded target polynucleotide hybridized to such adapter-ligated single-stranded first primer extension product. In some cases, the removing un-ligated adapters includes resin (e.g., silica (e.g., silica bead)) or membrane-based column or batch purification of double-stranded DNA from single-stranded DNA or purification of a selected size of single or double stranded DNA from the reaction mixture. In some cases, the removing includes removing from a reaction mixture single or double-stranded DNA, or a combination thereof, having a size of less than about 100 bases or base pairs. In some cases, the removing includes removing from a reaction mixture single or double-stranded DNA, or a combination thereof, having a size of more than about 1,000 bases or base pairs. In some cases, the removing includes purifying from the sample adapter-ligated primer extension products or double-stranded DNA containing such adapter-ligated primer extension products, or a combination thereof, having a size of more than about 100 bases or base pairs and less than about 1,000 bases or base pairs.

In some embodiments, removing the un-extended immune cell receptor V or C gene specific primers includes contacting the sample with an exonuclease. In some embodiments, the exonuclease has a single-strand degrading activity and lacks the double-strand degrading activity. In some embodiments, the exonuclease is thermolabile. In some embodiments, the exonuclease is Exonuclease I.

In some embodiments, the nuclease-protecting modification of universal amplification primers used in the amplification step allows to advantageously skip a purification step between the second primer extension and universal amplification thus saving time, resources and reducing the possibility of sample contamination.

In some embodiments, the method includes: e), hybridizing a plurality of immune cell receptor J gene specific primers (i.e., second primers) to the J region portions of the extended immune cell receptor V gene specific primers (i.e., first primer extension products), wherein the immune cell receptor J gene specific primers comprise a 3′ J gene hybridizing region and a 5′ second universal adapter region or hybridizing a plurality of immune cell receptor V gene specific primers (i.e., second primers) to the V region portions of the extended immune cell receptor C gene specific primers (i.e., first primer extension products), wherein the immune cell receptor V gene specific primers comprise a 3′ V gene hybridizing region and a 5′ second universal adapter region; and, f) extending the hybridized immune cell receptor J gene specific primers or extending the immune cell receptor V gene specific primers with a polymerase, thereby forming a plurality of structurally different double-stranded products comprising an extended immune cell receptor J gene specific primer or extended immune cell receptor V gene specific primer (i.e., second primer extension product) hybridized to an (e.g., adapter-ligated) extended immune cell receptor V gene specific primer or extended immune cell receptor C gene specific primer, each double-stranded product comprising at least a portion of the immune cell receptor V region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor J region flanked by a first and second universal adapter sequence or at least a portion of the immune cell receptor C region, optionally the immune cell receptor D region, and at least a portion of the immune cell receptor V region flanked by a first and second universal adapter sequence.

In some embodiments, the e) hybridizing and f) extending can be repeated multiple times by heating to denature double-stranded products produce in the extending of f) (e.g., double-stranded DNA products comprising first primer extension products (e.g., adapter-ligated extended immune cell receptor V or C gene specific primer) hybridized to second primer extension products (e.g., extended immune cell receptor J or V gene specific primer)), cooling to hybridize un-extended second primers to first primer extension products (e.g., adapter-ligated first primer extension products), and extending hybridized primers. In some cases, e) and f) are repeated 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more times. In some cases, e) and f) are repeated from 2 to 15 times, from 3 to 12 times, from 5 to 10 times, or from 5 to 15 times.

As described herein after extension of hybridized second primers, a polynucleotide containing at least a portion of a J-region, an optional D region, an optional C region, and at least a portion of a V region, flanked by universal primer binding sites, or a complement thereof is provided. This polynucleotide can be amplified by universal PCR with an amplification reaction mixture containing the polynucleotide, a forward universal primer and a reverse universal primer.

In some embodiments, extension of the second primer is performed in the presence of the opposite-facing primer hybridizing to the primer-binding site introduced into the primer extension product by the first primer.

In some embodiments, the second primer extension step comprises two or more repetitions of the annealing step. In some embodiments, the annealing step comprises a temperature profile including several (e.g., 2, 3 or more) annealing temperatures. In some embodiments, the annealing temperature profile comprises a series of decreasing temperatures. In some embodiments, the annealing step comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 20 or more rounds of thermocycling through the series of two or more annealing temperatures. In some embodiments, by way of example, the annealing step comprises 20 cycles wherein each cycle consists of an incubation at 60° C., at 57.5° C. and at 55° C.

In some embodiments, the second primer extension step comprises a round of initial denaturation, two or more rounds of: denaturation, step-wise annealing and extension, and a round of final extension. In some embodiments, by way of example, the second primer extension step comprises 10 cycles.

In some embodiments, the second primer extension step utilizes the following temperature profile: [initial denaturation]-[two or more rounds of: denaturation, annealing temperature profile, extension]-[final extension]. By way of example, the following thermal profile may be used.

Stage Temp (° C.) Duration Cycles Initial Denaturation 95° C. 5 min 1 Denature 95° C. 30 sec 10 Annealing high 60° C. 10 sec Annealing mid 57.5° C. 10 sec Annealing high 55° C. 10 sec Extension 72° C. 45 sec Final Extension 72° C. 1 min 1 End 4° C. ∞ 1

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, one of skill in the art will appreciate that many modifications and variations of this invention can be made without departing from its spirit and scope, as will be apparent to those skilled in the art. The specific embodiments described herein are offered by way of example only and are not meant to be limiting in any way. It is intended that the specification and examples be considered as exemplary only, with the true scope and spirit of the invention being indicated by the following claims.

All publications, patents, patent applications or other documents cited herein are hereby incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, or other document was individually indicated to be incorporated by reference for all purposes. Where a conflict exists between the instant application and a reference provided herein, the instant application shall dominate.

In some embodiments, the method further comprises contamination removal or reducing the amount of contaminating sequences in the sequencing data output. As disclosed herein, the contamination filtering process is a novel combination of physical steps and analytical steps. The inventors have observed that during amplification, a library may become contaminated by a nucleic acid fragment also containing universal amplification primer binding sites. For example, a fragment from another library or a pool of libraries may contaminate a reaction mixture described herein. In one embodiment, the primer extension target enrichment method disclosed herein includes a method of detecting and removing from sequencing data output the sequencing data originating from contaminating nucleic acids, the method comprising: 1) an increased number of primer extension cycles in the first round of primer extension; alone or in combination with 2) one or more rounds of exponential amplification in the second round of primer extension. The inventors have discovered that these extra rounds increase the ratio of true targets to contaminants in the sample subjected to sequencing and facilitate detection and removing of the sequencing data originating from the contaminants from the sequencing data output. The additional rounds of extension and added pre-amplification steps will increase the proportion of UMI (unique molecular index) family sizes of true targets in a mixture comprising true targets and contaminants. The proportions of molecule counts (by UMI sequences) are maintained by PCR, and sequencing. Therefore at the completion of sequencing, the contaminant reads appear as a much smaller population within the sequencing data output. In some embodiments, a bi-modal UMI family size distribution is obtained (FIG. 11 ). For example, 8 rounds of amplification lead to an observed 16-fold difference between the contaminant and an a target (FIG. 12 : 64 reads vs. 1024 reads).

In some embodiments, the method further comprises after sequencing, a step of calculating the number of nucleic acid sequences belonging to a UMI family (a group of nucleic acid sequences sharing an identical UMI). In some embodiments, the method further comprises identifying and retaining in the sequencing data output the top 90% of UMI families by size. In some embodiments, the method further comprises identifying and retaining in the sequencing data output the top 91%, 92%, 93%, 94%, 95% 96%, 97%, 98% or 99% of UMI families by size. In some embodiments, the method further comprises removing from the sequencing data output the bottom 10% of UMI families by size. In some embodiments, the method further comprises removing from the sequencing data output the bottom 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% of UMI families by size.

In some embodiments, the number of primer extension cycles in the first round of primer extension and the number of primer extension cycles in the second round of primer extension may be selected to optimize the calculation described above. The inventors have found that selecting optimal proportions of first round and second round primer extension may decrease the amount of the output that needs to be removed in the aforementioned calculation step. In some embodiments, 10 primer extension cycles may be performed in the first round and 20 primer extension cycles may be performed in the second round in order to minimize the output data that needs to be removed when calculating the number of nucleic acid sequences belonging to a UMI family. For example, when 10 first round primer extension cycles and 20 second round primer extension cycles are performed, the method may require removing less than the bottom 10% of UMI families by size.

Examples Example 1: Experimental Protocol—Immuno-PETE using gDNA from human PMBC

An schematic of an exemplary embodiment of immuno-PETE is illustrated in FIG. 1 .

A pool of primers selected from SEQ ID NOS:1-121 (i.e., first primer pool (gPE primer mix)) and a pool of the primers selected from SEQ ID NOS: 122-204 (i.e., second primer pool (PE2 primer mix)) were generated. The concentration of primers in each primer pool was adjusted to 100 μM, and the pools were diluted to a working concentration of 12 μM. As a control, a target enrichment method using a previously tested panel of oncology related nucleic acid probes was analyzed in a separate reaction. Input human PMBC genomic DNA was used at 100 ng per reaction. Reaction mixtures were prepared and incubated as depicted below, in Table 3.

TABLE 3 Primer Hybridization Mix Reagent Vol (μl) Isothermal Amp Buffer (10×) 4 dNTPs (10 mM) 1 gPE primer mix (100 uM) 2 MgCl2 (25 mM) 6 total 13

Aliquot 13 μl of Primer Hybridization Mix into each reaction tubes

Add water and samples to reaction tubes and mix as indicated above in the table

Place in thermocycler and run program Hyb and Extend 7-28

Polymerase Master Mix

Reagent Vol (μl) Water 8 Isothermal Amp Buffer (10×) 1 NEB Bst 2.0 (8 U/ul) 1 total 10

At 60° C. hold step, add 10 μl Polymerase Master Mix in each tubes and mix

Go to run, edit, skip step and continue with run program Hyb and Extend 7-28

Add Exonuclease 1 to samples 1 μl

Run program Exo 1 7-28

Perform AMPure clean up at 1.4 ratio

KAPAPure to add 70 Elution Volume 20

Ligation Master Mix

Reagent Vol (ul) Water 3.9 T7 Ligase Buffer (2×) 25 T7 DNA ligase (3000 U/μl) 0.1 total 29

Aliquot 29 μl Ligation Master Mix in each reaction tube

Add 20 μl gPE Extension Product and Mix

Add 1 μl of C7/P7 BC (Barcode) adapter (25 uM)

Incubate at 25° C. for 5 minutes

Add 50 μl of water to reach a volume of 100 μl

Perform AMPure clean up at 0.7× ratio

KAPAPure to add 70 Elution Volume 18

Primer Extension 2 PE2 Master Mix

Reagent Vol (ul) Phusion Mix (2×) 25 PE2 primer mix (20 uM) 2 Ammonium sulfate (200 mM) 5 total 32

Aliquot 32 μl PE2 Master Mix in each reaction tube

Add 18 μl Ligation Product and Mix

Place in thermocycler and run program PE2 for 15 Cycles

Perform AMPure clean up at 1× ratio

KAPAPure to add 50 Elution Volume 20

PETE CR Master Mix—50 uL

Reagent Vol (μu) Water 4 Phusion Mix (2×) 25 C5/C7 primer Mix (10 uM) 1 total 30

Add 20 μl of the Primer extension 2 product

Place in thermocycler and run program PETE CR

Perform AMPure clean up at 0.9× ratio

KAPAPure to add 45 Elution Volume 20

Thermal Cycling Protocols are depicted in Table 4.

TABLE 4 I. Hyb and Extend 7-28 Program II. 98° C.-2 minutes III. 80° C.-0 seconds IV. 60° C.-20 minutes V. 60° C.-hold VI. 65° C.-2 minutes VII. 80° C.-10 minutes VIII.  4º C.-hold IX. Exo I 7-28 Program X. 37° C.-10 minutes XI. 80° C.-10 minutes XII.  4° C.-hold XIII. PE2 Program XIV. 98° C.-1 minute i.15 cycles XV. 98° C.-10 seconds XVI. 80° C.-20 seconds XVII. 64° C.-20 seconds XVIII. 72° C.-30 seconds XIX.  4° C.-hold XX. PETE CR Program XXI. 98° C.-1 minute XXII. 24 cycles XXIII. 98° C.-10 seconds XXIV. 60° C.-20 seconds XXV. 72° C.-30 seconds XXVI.  4° C.-hold

Immuno-PETE reactions were analyzed by agarose gel electrophoresis (FIG. 2 ). The TCR library (generated with first primers (selected from SEQ ID NOS: 1-121) and second primers (selected from SEQ ID NOS:122-204) and RH-4 library (generated with the oncology panel of probes (Control)) were diluted to a final concentration of 4 nM, and pooled in a 4:1 ratio of TCR to RH-4 for Illumina sequencing. Sequencing was performed on the Illumina MiSeq instrument using paired-end 2×250 cycle sequencing. Over 15 million filtered pass reads were generated and analyzed.

Results:

The results of the TCR library and RH-4 library are summarized in Table 5.

TABLE 5 Sequencing Summary Analysis Imaging Summary Indexing Reads mapped to Index Id % Reads Total Identified Reads PF Reads (PF) CV Min Max 15805692 15271036 85.4589 0.8277 17.7223 157.7366 Index Index Index % Reads Number Sample Id Project 1 (17) 2 (15) Identified (PF) 1 TCR-PETE NA ATCACG 67.7366 2 RH4-PETE NA TGACCA 17.7223

A random subsample of 150,000 sequences, corresponding to 50× the expected number of different V(D)J sequences in the input genomic sample, was further analyzed. This subsample of sequencing data was de-duplicated. The de-duplicated (12K) and de-deduplicated (150K) data were processed to identify polynucleotides containing rearranged V(D)J regions. The results are summarized in Table 6.

TABLE 6 TCR Alignment Result Total_ % TCRB_ Total_ reads_ input_ Dup- Unas- productive_ input_ pairs_ reads_ Unique_ licate_ signed_ %_Dup- Con- unique_ read_ after_ after_ read_ read_ read_ licate_ sensus_ consensus_ Shannon_ Sample pairs filtering filtering pairs pairs pairs Rate reads reads Clones d50 entropy TCR- 150000 139654 93.1 2376 127231 10018 98.2 1699 174 108 0.96296296 100.8085935 PETE_1_ sampled 50x TCR-  12000  11178 93.2 1418 8955 803 86.3 1081 105 99 0.97979798  98.0031575 PETE_S1_ sampled_4x

Out of the 1081 sequences assigned in the 12 k sample to 99 clones, 100% have the same clone assigned when they were present in the 150 k set. There were in total 108 clones assigned to both sets, with 99 clones overlapping between the two sets. A Venn diagram of the overlap between the 12 k set and the 150 k set is depicted in FIG. 3 .

An analysis of top ranked TCR clones from the sample before and after de-duplication showed that the ranking can change as a result of de-duplication, as shown in Table 7.

TABLE 7 Top 10 ranking clones for TCRαß and TCRγδ isotypes (TRA-Top10-Non-Dedup SEQ ID NO: 214-223; TRA-Top10-Dedup: SEQ ID NO 244-253; TRB-Top 10-Non-Dedup: SEQ ID NO 224-233; TRB Top10-Dedup: SEQ ID NO:254-263; TRG-Top10-Non-Dedup: SEQ ID NO: 234-243; TRG-Top 10- Dedup: 264-273) TRA-Top10-Non-Dedup TRA-Top10-Dedup Clone Clone Rank Clone Rank Clone  1 TRAV27*_TRAJ42*_CAGGGSQGNLIF  1 TRAV27*_TRAJ42*_CAGGGSQGNLIF  2 TRAV12-2*_TRAJ43*_WPTGMRF  2 TRAV12-2*_TRAJ43*_WPTGMRF  3 TRAV38-1*_TRAJ33*_CAFMTPDSNYQLIW  3 TRAV38-1*_TRAJ33*_CAFMTPDSNYQLIW  4 TRAV21*_TRAJ45*_CAVGGYSGGGADGLTF  4 TRAV21*_TRAJ45*_CAVGGYSGGGADGLTF  5 TRAV25*_TRAJ28*_CAGSGAGSYQLTF  5 TRAV25*_TRAJ28*_CAGSGAGSYQLTF  6 TRAV1-2*_TRAJ27*_CAVSTNAGKSTF  6 TRAV13-1*_TRAJ18*_CAAKGRGSTLGRLYF  7 TRAV13-1*_TRAJ18*_CAAKGRGSTLGRLYF  7 TRAV27*_TRAJ42*_CAGGGSQGNLIF  8 TRAV27*_TRAJ42*_CAGGGSQGNLIF  8 TRAV1-2*_TRAJ27*_CAVSTNAGKSTF  9 TRAV26-1*_TRAJ47*_CIVRVVEYGNKLVF  9 TRAV26-1*_TRAJ47*_CIVRVVEYGNKLVF 10 TRAV5*_TRAJ4*_CAESEDSGGYNKLIF 10 TRAV13-2*_TRAJ13*_CAEMAPGGYQKVTF TRB-Top10-Non-Dedup TRB-Top10-Dedup Clone Clone Rank Clone Rank Clone  1 TRBV19*_TRBJ2-7*_CASSIRSSYEQYF  1 TRBV19*_TRB12-7*_CASSIRSSYEQYF  2 TRBV4-3*, TRBV4-2*_TRBJ2-1*_  2 TRBV4-3*, TRBV4-2*_TRB12-1*  CASSLLSYNEQFF CASSLLSYNEQFF  3 TRBV20-1*_TRBJ2-7*_CSAPRTSGGLLNPYEQYF  3 TRBV20-1*_TRBJ2-7*_CSAPRTSGGLLNPYEQYF  4 TRBV7-9*_TRBJ2-7*_CASSSQEAGGRYNSYEQYF  4 TRBV5-1*_TRBJ2-7*_CASSLEGQASSYEQYF  5 TRBV7-8*_TRBJ2-5*_CASSLKRDGQETQYF  5 TRBV7-8*_TRBJ2-5*_CASSLKRDGQETQYF  6 TRBV5-1*_TRB12-7*_ CASSLEGQASSYEQYF  6 TRBV7-9*_TR812-7*_CASSSQEAGGRYNSYEQYF  7 TRBV3-1*, TRBV3-2*_TRBJ2-3*_CASSLGTDTQYF  7 TRBV7-2*_TRBJ2-2*_CASSLGVGTGELFF  8 TRBV7-2*_TRBJ2-2*_CASSLGVGTGELFF  8 TRBV3-1*, TRBV3-2*_TRBJ2-3*_ CASSLGTDTQYF  9 TRBV7-9*_TRB12-7*_CASSSEIGTAGTSHNRQYF  9 TRBV28*_TRB12-7*_CASSLDRNEQYF 10 TRBV19*_TRBJ2-7*_CASSVRSSYEQYF 10 TRBV19*_TR812-7*_CASSVRSSYEQYF TRG-Top10-Non-Dedup TRG-Top10-Dedup Clone Clone Rank Clone Rank Clone  1 TRGV9*_TRGJ2*, TRGJ1*_CALWEVPHYYKKLF  1 TRGV9*_TRGJ2*, TRGJ1*_CALWEVPHYYKKLF  2 TRGV4*_TRGJ2*, TRGJ1*_CADQPQAYKKLF  2 TRGV4*_TRGJ2*, TRGJ1*_CADQPQAYKKLF  3 TRGV9*_TRGJP1*_CALWDETGWFKIF  3 TRGV9*_TRGJP1*_CALWDETGWFKIF  4 TRGV11*_ TRGJP1*_CACWIRHVRATGWFKIF  4 TRGV11*_TRGJP1*_CACWIRHVRATGWFKIF  5 TRGV5*, TRGV3*_TRGJ2*, TRGJ1*_   5 TRGV5*, TRGV3*_TRGJ2*, TRGJ1*_ CATWDRPEKLF CATWDRPEKLF  6 TRGV3*, TRGV5*_TRGJ2*, TRGJ1*_  6 TRGV3*, TRGV5*_TRGJ2*, TRGJ1*_ CATWDNPYYKKLF CATWDNPYYKKLF  7 TRGV3*, TRGV5*_TRGJ2*, TRGJ1*_  7 TRGV3*, TRGV5*_TRGJ2*, TRGJ1*_ CATWDSLYYKKLF CATWDSLYYKKLF  8 TRGV9*_TRGJP1*_CALWEVLTLSRTTGWFKIF  8 TRGV4*_TRGJ2*, TRGJ1*_CATCLYYKKLF  9 TRGV10*_TRGJP1*_CAAHTTGWFKIF  9 TRGV9*_TRGJP1*_CALWEVLTLSRTTGWFKIF 10 TRGV4*_TRGJ2*, TRGJ1*_ CATCLYYKKLF 10 TRGV10*_TRGJP1*_CAAHTTGWFKIF

Example 2: Experimental Protocol—RNA or mRNA Based Immuno-PETE

A modification of the immuno-PETE assay (e.g., as set forth in Example 1) is provided for starting material comprising total RNA or purified mRNA. Total RNA or purified mRNA can be obtained from whole blood, PBMC, sorted lymphocytes, lymphocyte culture, fresh or fresh-frozen tumor tissue, FFPE tissue samples, and the like. A schematic outlining an exemplary method for RNA or mRNA based immuno-PETE is set forth in FIG. 4 . Briefly, a cDNA synthesis step is introduced prior to the immuno-PETE method essentially set forth in Example 1.

Here, an oligo-dT primer, set of random primers (e.g., hexamers, heptamers, octamers or nanomers, etc.,) or one or more C-segment primers (e.g., comprising one or more C-segment primers selected from SEQ ID NOS:205-213; see Table 8) is added to an aliquot of total RNA or purified mRNA to form a reaction mixture. A reverse transcriptase (e.g., SuperScript III™) and amplification components (such as buffers, dNTPs and salts (e.g., MgCl₂)) is added to the reaction mixture to initiate first and second strand synthesis to form double-stranded cDNA molecules. The cDNA molecules can be purified, for example using SPRI beads, and quantified for later use. The purified cDNA is then used as a starting template for the Immuno-PETE protocol set forth in Example 1. For example, purified cDNA is used as a starting template and a V gene specific probe set (e.g., comprising SEQ ID NOS:1-121) is used in the first round of extension (gPE primer pool), followed by second round of extension using the C-segment probe set (PE2 primer pool, e.g., comprising SEQ ID NOS:205-213). Alternatively, the first round of extension can include use of the C-segment gPE primers, followed by a second round of extension using the plurality of V gene specific PE2 primers (e.g., comprising SEQ ID NOS:122-204).

Several advantages are achieved through the application of a cDNA synthesis step to the immuno-PETE assay (e.g., as described in Example 1) including (1) improved assay sensitivity (more copies of immune receptor mRNA exist in immune cells as compared to the single copy of somatically rearranged V(D)J locus in genomic DNA); (2) decrease in amplification bias (use of fewer C-segment primers/probes as compared to J-segment primers/probes in the immuno-PETE protocol of Example 1); (3) identification of immune receptor isotypes (resulting amplions from the RNA or mRNA based Immuno-PETE assay span the V(D)J immune receptor domain. For TCR, there are α-1, β-1 and β-2 constant genes. For immunoglobulins, the distinguishable isotypes are κ and λ for light chains, and IgA, IgD, IgG, and IgM for the heavy chains). As such, the total RNA and/or mRNA based immuno-PETE assay is advantageous for high-throughput sequencing and/or immune repertoire profiling.

TABLE 8 Sequence Sequence ID name Sequence 5′→3′ 205 IgM GATGGAGTCGGGAAGGAAGTCCTGTGCGAG 206 IgG GGGAAGACSGATGGGCCCTTGGTGG 207 IgA CAGGCAKGCGAYGACCACGTTCCCATC 208 IgD CCACAGGGCTGTTATCCTTT 209 IgE AGGGAATGTTTTTGCAGCAG 210 Igκ CATCAGATGGCGGGAAGATGAAGACAGATG GTGC 211 Igλ CCTCAGAGGAGGGTGGGAACAGAGTGAC 212 TCRB GCTCAAACACAGCGACCTCGGGTGGGAACA  C 213 TCRA TCTCTCAGCTGGTACACGGCAGGGTCAGGG

Example 3: Combined Immuno-PETE and Oncology Targets Panel

In immuno-oncology applications, it would be advantageous to profile both the somatic mutations in a tumor cell genome and the clonotype repertoire of tumor infiltrating T-cells, using a sample of tumor tissue (e.g., tumor biopsy or FFPE tumor tissue). Designing and optimizing such an assay by repeated design of multiple opposing (forward and reverse) multiplex-PCR primers is not practical. However, Immuno-PETE minimizes probe-probe (or primer-primer) interactions by using a design algorithm that separately designs gPE probe sets and PE2 probe sets to minimize primer dimers. The design algorithm can also place primers on +/− strands of genomic DNA such that primers are not pointed toward each other in the same reaction step, to prevent production of a shorter target. A further feature of the immuno-PETE assay is that each of the two probe hybridization and extension steps of the assay occur in separate (distinct) reactions after removal of residual probes from the previous step. Here, we demonstrate the immuno-PETE assay efficiently targets cancer genes and T-cell receptors in a combined assay, without prior optimization of the combined probe set, where there was no overlap or probe coordinates between the Oncology and TCR gene targets.

Experimental Design:

In order to demonstrate the utility of enriching both tumor cell genome targets and the somatically rearranged TCR targets from immune cells, we combined an oncology panel (Signature or “Sig” panel) containing 181 target regions from 21 cancer genes with a panel of V (n=60) and J (n=13) gene probes targeting TCRB. Specifically, SEQ ID NOS:1-60 were used as the V-gene probes and SEQ ID NOS:188-200 were used as the J-gene probes. Each of the panels was tested independently, but no attempts were made to optimize the combined probe set, all probes were used at equimolar concentrations.

Protocol:

Human genomic DNA (Promega Cat #G1471) was used as an input at 100 ng or 450 ng per reaction. This DNA sample is a mixture from multiple donors; it is not expected to contain oncology relevant somatic mutations, and assuming it has been isolated from PBMC, it contains T-cell genomic DNA. TCRB repertoire is expected to be very diverse due to the pooled nature of the DNA sample. Reaction mixtures were prepared and incubated as set forth in Table 9.

TABLE 9 Qiagen Multiplex Tag and Phusion HS2 MM (16 + 1 samples) Reagent Vol (ul) Water 1.5 2× (Taq or Phusion) Master Mix 12.5 gPE Mix Signature, +Fix, +TCRB 1 Sheared gDNA template (10 ng/ul, 45 ng/ul) 10

-   -   Mix and place into thermal cycler     -   Run program <gPE Taq-Hyb Extend>     -   Remove tubes from the thermal cycler     -   Add 1 ul of Exonuclease I to the sample and mix     -   Place into thermal cycler     -   Run program <Exonuclease & Heat Kill>     -   Remove tubes from the thermal cycler     -   Prepare ligation master mix         Ligation Master Mix (6+1 samples)

Reagent Vol (ul) 2× ligase Buffer 25 T7 DNA ligase (30 U/μl) 1

-   -   Add 25 ul to the sample and mix     -   Add 1 uL of barcoded adapter to each sample     -   Place into thermal cycler     -   Run program <Ligation>     -   Prepare KapaPure Reagent for ligation Cleanup         KapaPure Reagent for Ligation Cleanup (6+1 samples)

Reagent Vol (ul) KapaPure or Am pure 70 H2O 50

-   -   Remove tubes from the thermal cycler

Add 120 uL KapaPure Reagent for Ligation Cleanup to the sample Completely mix by vortexing or pipetting Pop spin tubes to get oil droplets off of tube cap Incubate at room temperature for at least 2 minutes Place on magnet until beads are completely on sidewall Completely remove supematant and discard Wash 2 times with 180 uL of 85% ethanol Completely remove ethanol and dry pellet for 5 minutes Resuspend m 10 uL of 10 mM Tris pH 8.0 PE2 Reagent Mix (6+1 samples)

Reagent Vol (ul) Phusion HF Mix (2×) 25 XC7/LP5-8 10 uM each 2 Ammonium sulfate (200 mM) 5 ETSSB 1 PE2 primer mix 12 uM 1 Betaine 5M 6 Sample 10

-   -   Place into thermal cycler     -   Run program <PE2_PETE-CR>

gPE Tag-Hb Extend SOP

Step Temperature Time Initial Denaturation 95° C.  5 min Annealing 54º C. 30 minutes Extension 68° C.  2 min End 4° C. Hold (∞)

Exonuclease 37° C. 10 min

Step Temperature Time Exonuclease 37° C. 10 min Heat Kill 75° C. 10 min End 4° C. Hold (∞)

PE2 PETE-CR SubCyc 55-65

Step Temperature Time Initial Denaturation 98° C.  1 min Denaturation 98° C. 10 sec Annealing (ramp at 0.2° C./sec) 55° C. 30 sec 5× Annealing low 55° C. 30 sec 4× Annealing high 65° C. 30 sec Extension 72° C. 30 sec Denaturation 98° C. 10 sec n Annealing 64° C. 15 sec Extension 72° C. 72° C. 30 sec Stop 4° C. Hold (∞) n = 20 cycles for 100 ng n = 18 cycles for 450 ng

Results:

After completion of the immuno-PETE protocol set forth in Table 9, an aliquot of the reaction products from the 100 ng and 450 ng input gDNA was analyzed by agarose gel electrophoresis (FIG. 5 ). In FIG. 5 , lanes 1-8 correspond as follows, lane 1: MW ladder; lanes 2,3: Oncology panel only, 100 ng gDNA; lanes 5, 6: Oncology panel only, 450 ng gDNA; lane 4: Oncology panel+TCRB, 100 ng gDNA; lane 7: Oncology panel+TCRB, 450 ng gDNA; lane 8: No Template (NT), negative control.

The enriched libraries were sequenced using Illumina MiSeq sequencer and Illumina MiSeq sequencing kit v3 using 2×300 cycles as per manufacturer's protocols. Sequencing analysis:

Analysis of oncology targets in the combined panel assay are provided in Table 10. A total of 543,000 read pairs for each of the 100 ng and 450 ng input gDNA was assessed. For the 450 ng gDNA sample a total of 153,138 unique pairs were identified. By comparison, 118,098 unique pairs were identified in the 100 ng gDNA sample. Additionally, analysis of the TCRB targets in the combined panel assay for each of the 100 ng or 450 ng input gDNA are summarized in Table 11.

TABLE 10 PETE SW Mean Total % UIDs Total read Deduped Deduped Dedup Dedup per % input pairs trimmed trimmed On- % non- Median bases >= Uniformity read after UNIQUE % reads reads target On- zero target 100x (0.5x-2x of Sample pairs filtering pairs Duplicate mapped mapped reads target probe coverage Coverage mean) 450 ng- 543000 520443 153138 68.2 152217 29.2 138948 91.3 846.1 1367 99.9 81.2 Sig- TCRb_ S6L00 100 ng- 543000 522924 118098 75.2 117291 22.4 101989 87   652.5  970 99.6 77.9 Sig- TCRb_ S5L00

TABLE 11 (SEQ ID NO: 318-337) Total_ %_input_ TCRB_ Total_ reads_ reads_  Dup- Un- productive_ input_ pairs_ after_ Unique_ licate_ assigned_ % unique_ read_ after_ filter- read_ read_ read_ Duplicate_ Consensus_ consenus_ Shannon_ Sample pairs filtering ing pairs pairs pairs Rate reads reads d50 entropy 100 ng- 3036337 2923802 96.3 748 8265 2912059 91.7 747 85 0.97619048 83.6249492 Sig- TCRb_ S5_L001 Clone Clone AA. Seq. CDR3 count fraction 2 0. CATSRGSPNYGYTF 02352941 1 0. CASSPGTSGSASSTDTQ 01176471 YF 1 0. CASSLALIVGGENTEAF 01176471 F 1 0. CASSKGGTGGGWAGE 01176471 LFF 1 0. CASSQAFLPSLVTDTQ 01176471 YF 1 0. CASSADTGTFMNTEAF 01176471 F 1 0. CASSLGERGALSETQY 01176471 F 1 0. CASSFSKN 01176471 SRPYNEQFF 1 0. CASSLGSRGQRLLEQY 01176471 F 1 0. CASSLVAGGFSYNEQF 01176471 F 450ng· 1393309 1335599 95.9 580 2904 1330803 83.4 569 140 0.98550725 137.254685 Sig. TCRb_S6_ L001 Clone Clone AA. Seq. CDR3 count fraction 2 0. CASSPGTGIDTQYF 01428571 2 0. CASSRQGNSPLHF 01428571 1 0. CASSQGRTRLQRGGRT 00714286 DTQYF 1 0. CASSIGLAGALRDTGEL 00714286 FF 1 0. CASSLRGPGQGEGGSP 00714286 LHF 1 0. CASSYPFPLTGGNQPQ 00714286 HF 1 0. CASSYAGTRLGNQPQH 00714286 F 1 0. CASSLGLAGVRQETQY 00714286 F 1 0. CASSLNRAFSGANVLT 00714286 F 1 0. CASSEARSGPDTDTQY 00714286 F

Here, the data demonstrates the potential of immuno-PETE assays to sequence both oncology targets in the tumor cell genome and the clonotype repertoire of tumor infiltrating T-cells. The combined assay is a single tube reaction requiring as little as 100 ng DNA input, thus making it suitable for analysis of tumor tissue biopsies or FFPE tissue samples in immuno-oncology applications.

Immune-sequencing assays compatible with clinically relevant sample types, such as enriched T cell population or formalin fixed paraffin embedded tissue (FFPE) would provide valuable clinical utility.

Example 4 demonstrates Immuno-PETE, as described herein, in the context of FACS sorted T cells; while Example 5 demonstrates Immuno-PETE in the context of FFPE tissue cells.

Example 4: Immuno-PETE Using Antigen Positive FACS Sorted Human T-Cells

Experimental Design:

The amino acid sequences of CDR3 were determined for T cell receptor alpha and beta chains. Here, Immuno-PETE was performed essentially as set forth in Example 1 with DNA extracted from formalin fixed human T cells that were FACS sorted for M1 antigen (using 113 ng, 57 ng, or 11 ng DNA input; see Table 12 and FIG. 6 ).

Results:

Clonotyping of T cell receptor alpha and beta chains was determined, see Table 12 and FIG. 6 .

TABLE 12 Sample type ng T cell count * FACS sorted M1 specific T cells 113 18,880 57 9,440 11 1,888 FFPE 90% Tumor 10% M1 specific T cells 27 443 6 100 * 1 TCR template per 6 pg of DNA

Conclusion:

This example demonstrated the ability to predict T cell receptor alpha and beta CDR3 sequences at low input amounts in FACS sorted T cells. The T cell population was highly clonal as expected, and the most frequently observed CDR3 sequences were the same for all input amounts, for both alpha and beta chains.

Here, the immuno-PETE assay utilized at most 113 ng DNA input and as little as 11 ng DNA input, thus making it very suitable for analysis of tumor tissue biopsies or FFPE tissue samples in immuno-oncology applications.

Example 5: Immuno-PETE Using FFPE Tissue Sample Experimental Design:

As in Example 4, the amino acid sequences of CDR3 were determined for T cell receptor alpha and beta chains. Here, human T cells that were FACS sorted for M1 antigen were mixed with adenocarcinomic human alveolar basal epithelial cells (A549) at 1:9 ratio. Mixed cells were pelleted and fixed with formalin and embedded in paraffin (FFPE). DNA was extracted from the sectioned FFPE cell pellet, and Immuno-PETE was performed essentially according to Example 1 with either 6 ng or 27 ng DNA input. The DNA input amount was determined with qPCR (KAPA Human Genomic DNA Quantification and QC kit, Catalog Number 07960590001, Roche Diagnostics Corp., IN, USA).

Results:

Clonotyping of T cell receptor alpha and beta chains was determined, see Table 12 and FIG. 7 .

Conclusion:

This Example demonstrates the ability to predict T cell receptor alpha and beta CDR3 sequences at low input amounts in FFPE tissue cells mixed with tumor cells (1:9 ratio). The T cell population was highly clonal as expected, and the most frequently observed CDR3 sequences were the same for both input amounts, for both alpha and beta chains.

Here, the immuno-PETE assay utilized less than 30 ng DNA input making it very suitable for analysis of tumor tissue biopsies or FFPE tissue samples in immuno-oncology applications.

Example 5. Improved Method of Immuno-PETE

In this experiment, genomic DNA was isolated from PBMC, PanT cells of Hut78 cell line. The first Primer Extension reaction had primers for V genes of: TCR-beta (69), immunoglobulin (immunoglobulin heavy chain, IGH) (138) and TCR-delta (8), the reaction contained:

Reagent Volume (ul) Kapa Long Range HotStart Ready Mix (2×) with Dye 12.5 V-gene primer mix (50 uM) 1 DMSO (to final volume in reaction of 5%) 1.25 sample gDNA(100 ng) 10.25 Total 14.75

The following thermocycling program was run:

Stage Temp (° C.) Duration Cycles Initial Denaturation 95° C. 10 min 1 Intermediate Temp 80° C. 0 sec Annealing (ramp at 0.2° C./sec) 60° C. 0 sec Annealing high 60° C. 20 sec 20 Annealing mid 57.5° C. 20 sec Annealing low 55° C. 20 sec Extension 72° C. 2 min 1 End 4° C. ∞ 1

A 1:5 dilution of Thermoabile Exonuclease I in nuclease-free water was made and added at 5 ul per sample. The following thermocycling program was run:

Temp (° C.) Duration 37° C. 4 min 80° C. 1 min  4° C. ∞

The first Kapa HyperPure bead purification was performed according to the manufacturer's instructions resulting in dry beads in each vial.

The second primer extension reaction had primers for J genes of: TCR-beta (14), immunoglobulin (immunoglobulin heavy chain, IGH) (9) and TCR-delta (4). The reaction also contained an opposite facing universal primer (Illumina i7 without barcode/index sequence). The reaction contained:

Reagent V (ul) Kapa Long Range HotStart Ready Mix (2×) with Dye 12.5 J-gene primer mix (20 nM) 2 i7-short (no index) primer 1 Nuclease-free water 9.5 Add to dry beads from 1^(st) primer extension Total 25

The following thermocycling program was run:

Stage Temp (° C.) Duration Cycles Initial Denaturation 95° C. 5 min 1 Denature 95° C. 30 sec 10 Annealing high 60° C. 10 sec Annealing mid 57.5° C. 10 sec Annealing high 55° C. 10 sec Extension 72° C. 45 sec Final Extension 72° C. 1 min 1 End 4° C. ∞ 1

The reactions proceed directly to library amplification. The library amplification reaction contained:

Reagent V (ul) Kapa Long Range HotStart Ready Mix (2×) with Dye 12.5 Nuclease-free water 2.5 Thermoable Exol (1:5 diluted) 5 Add to 2^(nd) primer extension reaction 25 Nuclease-protected i7/i5 indexed sequencing primers 5 Total 50

The following thermocycling program was run:

Stage Temp (° C.) Duration Cycles Reaction 37° C. 4 min 1 Initial Denaturation 95° C. 3 min 1 Denature 95° C. 30 sec 20 Anneal 57° C. 30 sec Extension 72° C. 45 sec Final Extension 72° C. 1 min 1 End 4° C. ∞ 1

The first Kapa HyperPure bead purification was performed according to the manufacturer's instructions. The quality and concentration of resuspended libraries were analyzed on Bioanalyzer and Qubit Quant. The following quality control standards were set for Immuno PETE:

-   -   1. The concentration of the libraries should be over 0.5 ng/ul     -   2. No or very few small fragments detected under 200 bp     -   3. No or few large fragments over 700 bp     -   4. Narrow peak for cell lines

The QC-pass libraries were pooled and sequenced on Illumina NextSeq instrument following manufacturer's instructions.

Example 6. Contamination Removal from Sequencing Data

In this example, contamination removal was applied to the sequencing reads obtained from a sample having nucleic acids isolated from PanT spiked with a contaminant from the Hut78 cell line. Primer extension was performed by the method of Example 5. The enriched nucleic acids were sequenced on Illumina NextSeq instrument.

The peak of 64 reads was observed corresponding to the contaminant. (FIG. 12 ). VDJ rearrangements and Clone Counts for all UMI families with >1 reads were obtained. Even after filtering UMI families sizes for >1 reads (replicates), 966 clones of the Hut78 sequence were observed contaminating the PanT sample. After filtering for the top 90% of UMI families (covered by 90% of the total clustered reads) a majority of the Hut78 clone sequences (UMI families) were filtered out and only 38 remained. The remainder of the VDJ recombinants left in the sample were sequences from the PanT sample.

While the invention has been described in detail with reference to specific examples, it will be apparent to one skilled in the art that various modifications can be made within the scope of this invention. Thus the scope of the invention should not be limited by the examples described herein, but by the claims presented below. 

What is claimed is:
 1. A method for enriching a sample for a plurality of structurally different target polynucleotides comprising an immune gene sequence the method comprising: a) contacting a sample with a plurality of immune cell receptor V gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT1], [BARCODE], and [V], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT] is a first adaptor sequence; [BARCODE] is a unique molecular identifier barcode; and [V] is a sequence capable of hybridizing to an immune cell receptor V gene; b) hybridizing and extending the V gene specific primers to form a plurality of first double-stranded primer extension products; c) contacting the sample with an exonuclease to remove unhybridized V gene specific primers from the first double stranded primer extension products; d) contacting the sample with a plurality of immune cell receptor J gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT2], and [J], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT2] is a second adaptor sequence; and [J] is a sequence capable of hybridizing to an immune cell receptor J gene; and further contacting the sample with a first universal primer capable of hybridizing to the first adaptor sequence; e) hybridizing and extending the J gene specific primers and the first universal primer to form a plurality of second double-stranded primer extension products; f) contacting the sample with an exonuclease to remove unhybridized J gene specific primers and first universal primer from the second double-stranded primer extension products; g) contacting the sample with first and second universal primers capable of hybridizing to the first and second adaptor sequences; h) amplifying the plurality of second double-stranded primer extension products thereby enriching the plurality of structurally different target polynucleotides comprising an immune gene sequence.
 2. The method of claim 1, wherein the immune genes comprise one or more of T-cell receptor alpha (TCRA), T-cell receptor beta (TCRB), T-cell receptor gamma (TCRG), T-cell receptor delta (TCRD), Immunoglobulin heavy chain (IGH), Immunoglobulin light chain-kappa (IGK) and Immunoglobulin light lambda (IGL).
 3. The method of claim 1, wherein the plurality of V gene specific primers and the plurality of J gene specific primers include primers from Table 2a.
 4. The method of claim 1, wherein hybridizing in steps b) and/or e) comprises one or more cycles of a step-wise temperature drop of two or more steps.
 5. The method of claim 4, wherein hybridizing in steps b) and/or e) comprises 20 cycles of temperature change from 60° C. to 57.5° C. and to 55° C.
 6. The method of claim 1, wherein hybridizing and extending in step e) comprises two or more cycles of duplex denaturation, primer annealing and primer extension.
 7. The method of claim 6, wherein primer annealing comprises one or more cycles of a step-wise temperature drop of two or more steps.
 8. The method of claim 7, wherein hybridizing and extending in step e) comprises 10 cycles temperature change from >90° C., to 60° C. to 57.5° C., to 55° C. and to 72° C.
 9. The method of claim 1, wherein the first and second universal primers in step g) comprise additional 5′sequences not present in the first and second adaptors.
 10. The method of claim 9, wherein the first universal primer in step d) does not comprise additional 5′sequences not present in the first adaptor.
 11. The method of claim 1, wherein the exonuclease in steps c) and/or f) is thermolabile.
 12. The method of claim 11, wherein the exonuclease is Exonuclease I.
 13. The method of claim 1, wherein extending in steps b) and/or e) is with a high-fidelity DNA polymerase.
 14. The method of claim 1, further comprising a purification step after steps c) and/or h).
 15. The method of claim 1, not having a purification step between steps f) and g).
 16. The method of claim 15, wherein the first and second universal primers comprise a modification preventing digestion of the primers with the exonuclease.
 17. The method of claim 16, wherein the primers comprise one or more nucleotides having a modification selected from: phosphorothioate (PS) bond, a 2′-O-methyl (2′OMe), a 2′-fluoride and Inverted ddT.
 18. The method of claim 1, wherein the V-gene specific primers, the J-gene specific primers and the first universal primer in step d) do not comprise a modification preventing digestion of the primers with the exonuclease.
 19. The method of claim 1, further comprising sequencing the plurality of structurally different target polynucleotides comprising an immune gene sequence.
 20. A method for contamination-reduced sequencing a plurality of structurally different target polynucleotides comprising an immune gene sequence the method comprising: a) contacting a sample with a plurality of immune cell receptor V gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT1], [BARCODE], and [V], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT] is a first adaptor sequence; [BARCODE] is a unique molecular identifier barcode (UMI); and [V] is a sequence capable of hybridizing to an immune cell receptor V gene; b) hybridizing and extending the V gene specific primers to form a plurality of first double-stranded primer extension products; c) contacting the sample with an exonuclease to remove unhybridized V gene specific primers from the first double stranded primer extension products; d) contacting the sample with a plurality of immune cell receptor J gene specific primers, each primer including from 5′ to 3′: [5′-Phos], [SPLINT2], and [ ], wherein: [5′-Phos] is a 5′ phosphate; [SPLINT2] is a second adaptor sequence; and [ ] is a sequence capable of hybridizing to an immune cell receptor J gene; and further contacting the sample with a first universal primer capable of hybridizing to the first adaptor sequence; e) hybridizing and extending the J gene specific primers and the first universal primer to form a plurality of second double-stranded primer extension products; f) contacting the sample with an exonuclease to remove unhybridized J gene specific primers and first universal primer from the second double-stranded primer extension products; g) contacting the sample with first and second universal primers capable of hybridizing to the first and second adaptor sequences; h) amplifying the plurality of second double-stranded primer extension products thereby enriching the plurality of structurally different target polynucleotides comprising an immune gene sequence; i) sequencing the plurality of structurally different target polynucleotides comprising an immune gene sequence to obtain a dataset of sequence reads; j) grouping the sequence reads having an identical UMI into UMI families; k) removing from the dataset UMI families with relative representation of less than 10%.
 21. The method of claim 20, wherein representation in step k) is less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1%.
 22. The method of claim 20, wherein the immune genes comprise one or more of T-cell receptor alpha (TCRA), T-cell receptor beta (TCRB), T-cell receptor gamma (TCRG), T-cell receptor delta (TCRD), Immunoglobulin heavy chain (IGH), Immunoglobulin light chain-kappa (IGK) and Immunoglobulin light chain-lambda (IGL).
 23. The method of claim 20, wherein the plurality of V gene specific primers and the plurality of J gene specific primers include primers from Table 2a.
 24. The method of claim 20, wherein hybridizing in steps b) and/or e) comprises one or more cycles of a step-wise temperature drop of two or more steps.
 25. The method of claim 24, wherein hybridizing in steps b) and/or e) comprises 20 cycles of temperature change from 60° C. to 57.5° C. and to 55° C.
 26. The method of claim 20, wherein hybridizing and extending in step e) comprises two or more cycles of duplex denaturation, primer annealing and primer extension.
 27. The method of claim 26, wherein primer annealing comprises one or more cycles of a step-wise temperature drop of two or more steps.
 28. The method of claim 27, wherein hybridizing and extending in step e) comprises 10 cycles temperature change from >90° C., to 60° C. to 57.5° C., to 55° C. and to 72° C.
 29. The method of claim 20, wherein the first and second universal primers in step g) comprise additional 5′sequences not present in the first and second adaptors.
 30. The method of claim 29, wherein the first universal primer in step d) does not comprise additional 5′sequences not present in the first adaptor.
 31. The method of claim 20, wherein the exonuclease in steps c) and/or f) is thermolabile.
 32. The method of claim 31, wherein the exonuclease is Exonuclease I.
 33. The method of claim 20, wherein extending in steps b) and/or e) is with a high-fidelity DNA polymerase.
 34. The method of claim 20, further comprising a purification step after steps c) and/or h).
 35. The method of claim 20, not having a purification step between steps f) and g).
 36. The method of claim 35, wherein the first and second universal primers comprise a modification preventing digestion of the primers with the exonuclease.
 37. The method of claim 36, wherein the primers comprise one or more nucleotides having a modification selected from: phosphorothioate (PS) bond, a 2′-O-methyl (2′OMe), a 2′-fluoride and Inverted ddT.
 38. The method of claim 20, wherein the V-gene specific primers, the J-gene specific primers and the first universal primer in step d) do not comprise a modification preventing digestion of the primers with the exonuclease. 